Production of reprogrammed pluripotent cells

ABSTRACT

The present invention provides a method of producing a reprogrammed cell, said method comprising exposing Stro-1 +  multipotential cells and/or progeny cells thereof to one or more potency-determining factors under conditions sufficient to reprogram the cells. The present invention also provides cells produced by such a method and cells differentiated therefrom in addition to various uses of those cells.

FIELD OF THE INVENTION

The present invention relates to pluripotent cells and methods for theirproduction.

BACKGROUND OF THE INVENTION

Embryonic stem (ES) cells can purportedly grow indefinitely whilemaintaining pluripotency and can differentiate into cells of all threegerm layers, i.e., mesoderm, endoderm and ectoderm (Evans & Kaufman,Nature 292: 154-156 (1981)). Human ES cells and cells derived therefromare currently being assessed for the treatment of a host of diseases,such as Parkinson's disease, spinal cord injury and diabetes. However,the fact that human ES cells are obtained from human embryos raises anumber of highly contentious ethical considerations and in manycountries the derivation of these cells is prohibited by law.Furthermore, because ES cells and cells derived therefrom expressantigens from the subject from which they are derived, there is a riskthat those cells will be rejected if administered to an unmatched (e.g.,not expressing similar HLA type(s) subject. Accordingly, scientists havesought technical solutions to avoid the current methods of generating EScells. One desirable way to accomplish these solutions would be togenerate pluripotent cells directly from somatic cells of a post-natalindividual, e.g., directly from a subject to be treated or a related orotherwise matched subject.

One method for reprogramming a somatic cells involves transferring thenuclear contents of the cell into an oocyte (Wilmut et al, Nature385:810-813(1997)) or by fusion with an ES cell (Cowan et al, Science309: 1369-1373 (2005)), indicating that unfertilized eggs and ES cellscontain factors that confer totipotency or pluripotency in somaticcells. Difficulties associated with these methods include therequirement for destruction of ova and/or embryos, which may raiseethical considerations in some countries.

Although the transcriptional determination of pluripotency is not fullyunderstood, several transcription factors, including Oct 3/4 (Nichols etal, Cell 95:379-391 (1998)), Sox2 (Avilion et al, Genes Dev. 17: 126-140(2003)) and Nanog (Chambers et al, Cell 113:643-655 (2003)) are involvedin maintaining ES cell pluripotency; however, none is sufficient aloneto specify ES cell identity.

Recently, Takahashi & Yamanaka introduced four factors (i.e., Oct4,Sox2, c-Myc and Klf4) into mouse ES cells and mouse adult fibroblastscultured under conditions suitable for mouse ES cell culture. Followingtransduction into either cell type, the authors obtained inducedpluripotent stem (iPS) cells that exhibited mouse ES cell morphology andgrowth properties and expressed mouse ES cell marker genes (Takahashi &Yamanaka, Cell 126:663-676 (2006)). Subcutaneous transplantation of iPScells into nude mice resulted in tumors containing a variety of tissuesfrom all three germ layers. Following injection into blastocysts, iPScells contributed to mouse embryonic development. These data demonstratethat pluripotent cells can be directly generated from mouse fibroblastcultures by adding only a few defined factors using a retroviraltransduction. However, this technique does suffer from some majordisadvantages, including a low rate of reprogramming (considerably lessthan 1% of treated cells), and the need for genomic integration andcontinuous expression of the oncogenes c-Myc and Klf4. Expression ofthese genes may lead to production of tumors in recipients of the cellsor cells derived therefrom. In this respect, chimeric mice producedusing iPS cells generated with these methods develop tumors, presumablyas a result of continuous expression of these oncogenes. Consequently, amajor goal of research in the field is to develop reprogramming methodsthat either do not require genomic integration of nucleic acids encodingthese factors or that minimize the number or duration of expression ofthese and other reprogramming factors.

While the majority of iPS cell-based studies use fibroblast cells, mostlikely due to their ease of derivation and extensive use in fusion-basedreprogramming studies various cell populations have been used for iPScell induction in the mouse other than fibroblasts. An importantobservation from these studies is that the somatic cell type selectedhad a significant effect on the efficiency of iPS cell generation andlevel of reprogramming. In this regard, some cell types, such as neuralstem cells, stomach cells and liver cells appear to reprogram atrelatively high efficiency compared to fibroblast cells. However,isolation of these cells from humans is difficult or not feasible due tothe invasive nature of tissue collection and/or limited donor samplesavailable. Some more accessible cell types (e.g., muscle cells ordifferentiated hematopoietic cells) have been used as the basis for iPSstudies, however reprogramming has met with limited success.

Accordingly, there is a need in the art for identifying optimal celltypes that are easily accessible and that reliably enable efficientreprogramming. Identifying such a cell type with efficient reprogrammingproperties would facilitate use of reprogramming methods without theneed for genomic integration and/or with a minimum or reduced number ofreprogramming factors. This would result in a safer pluripotent iPS cellpopulation with reduced risk for neoplastic transformation. Such celltypes, highly efficient for reprogramming and obtained without relyingupon embryonic tissues, would be suited for use in applications alreadycontemplated for existing, pluripotent ES cells.

SUMMARY OF INVENTION

In work leading up to the present invention, the inventor attempted toproduce iPS cells using cells from various sources, despite theconventional wisdom that many tissue sources are not suitable sourcesfor efficiently producing iPS cells. Surprisingly, the inventor foundthat Stro-1⁺ multipotential cells or progeny cells thereof(particularly, those from adipose tissue or dental pulp tissue) were auseful source for producing iPS cells with high efficiency, e.g., higherefficiency than fibroblasts.

The inventor also determined that Stro-1⁺ multipotential cells orprogeny cells thereof express endogenous factors normally needed to beadded exogenously to reprogram fibroblasts to produce iPS cells, e.g.,Klf4 and/or c-myc. Such endocgenous gene expression may permitproduction of iPS cells without introducing high levels of theseproteins or without introducing these non-endogenous forms of proteinsat all. The endogenous expression of c-myc may also facilitateproduction of iPS cells that have a reduced risk of tumorigenesis sincethey may not require constitutive and/or strong expression of thisoncogene.

One example of the invention provides a method for producing areprogrammed cell, said method comprising exposing Stro-1⁺multipotential cells and/or progeny cells thereof to one or morepotency-determining factors under conditions sufficient to reprogram thecells, and culturing the exposed cells to obtain reprogrammed cells.This method applies equally to a method for producing an inducedpluripotent stem (iPS) cell.

Another example of the present invention provides a method of producinga reprogrammed cell, said method comprising exposing a population ofcells enriched for Stro-1⁺ multipotential cells and/or progeny cellsthereof to one or more potency-determining factors under conditionssufficient to reprogram the cells.

The source of the Stro-1+ multipotential cells can be any tissue wherethese cells are located in situ. Preferably, the source of the Stro-1⁺multipotential cells is adipose tissue or dental pulp tissue. Anothersource of the Stro-1+ cells is bone marrow.

In one example, the Stro-1⁺ multipotential cells or progeny cellsthereof are enriched from adipose tissue, dental pulp tissue, bonemarrow, or other sites prior to exposure to the one or morepotency-determining factors.

In one example, the method of the present invention comprises culturingthe exposed cells to obtain reprogrammed cells which have broaderdifferentiation capabilities than the Stro-1⁺ multipotential cellsand/or progeny cells thereof, i.e., are capable of differentiating intoa broader range of cell lineages and/or cell types than Stro-1⁺multipotential cells and/or progeny cells thereof.

Exemplary potency determining factors include, but are not limited to, afactor individually or collectively selected from the group consistingof Oct4, Sox2, Klf4, Nanog, Lin28, c-Myc, bFGF, SCF, TERT, SV40 large Tantigen, HPV16E6, HPV16E7, Bmil, Fbx15, Eras, ECAT15-2, Tcl1, β-catenin,ECAT1, ESG1, Dnmt3L, ECAT8, Gdf3, Sox15, ECAT15-1, Fthl17, Sal14, Rex1,UTF1, Stella, Stat3, FoxD3, ZNF206, Myb12, DPP A2, Otx2 and Grb2 or acompound having the same or similar activity to one or more of saidfactors, e.g., an active fragment thereof or a small molecule. Anotherexemplary potency determining factor is a chemical, a peptide, a siRNA,a shRNA or a microRNA, e.g., as described herein. For example, the oneor more potency-determining factors are individually or collectivelyselected from the group consisting of:

(i) Oct4;

(ii) a combination of Oct4 and Sox2;(iii) a combination of Oct4, Sox2 and at least one of Nanog and Lin28;(iv) a combination of Oct4, Klf4 and c-Myc;(v) a combination of Oct4, Sox2 and Klf4;(vi) a combination of Oct4, Sox2, Klf4 and c-Myc;(vii) a combination of Oct4, Sox2, Nanog and Lin28;(viii) a combination of Oct4, Sox2, Klf4, c-Myc, Nanog and Lin28; and(ix) any one of (i) to (x) additionally in combination with a chemical,a peptide, a siRNA, a shRNA or a microRNA.

Preferably, the potency-determining factors are Oct4, Sox2, Klf4 andc-Myc.

In one example of the method of the present invention, the Stro-1⁺multipotential cells and/or progeny cells thereof are obtained from apost-natal subject. In accordance with this embodiment, the method canadditionally comprise obtaining or isolating the Stro-1⁺ multipotentialcells and/or progeny cells from the subject.

Preferably, the subject is a mammal and/or the cells are mammalian.Exemplary mammalian subjects include but are not limited to human,primate, livestock (e.g. sheep, cow, horse, donkey, pig), companionanimals (e.g. dogs, cats), laboratory test deer). Preferably the mammalis a human or primate. Most preferably the mammal is a human.

In one exemplary form of the invention, exposing the Stro-1⁺multipotential cells and/or progeny cells thereof to one or morepotency-determining factors comprises introducing nucleic acidcomprising a sequence encoding one or more potency-determining factorsoperably linked to a promoter into the Stro-1⁺ multipotential cellsand/or progeny cells thereof. A plurality of potency factor encodingnucleic acids can be distinct from one another or in a single nucleicacid, e.g., in a single expression vector comprising a plurality ofnucleic acids each linked to a separate promoter or each linked to asingle promoter, e.g., in a multi-cistronic vector. Preferably, thenucleic acids are contained within a vector, more preferably a viralvector, e.g., a retroviral vector or an adenoviral vector.

In one example of the present invention, the nucleic acid do(es) notintegrate into the genome of the Stro-1⁺ multipotential cells and/orprogeny cells thereof. For example, the nucleic acid(s) remain as one ormore episomes within the cell(s) and/or are eventually eliminated fromthe cell(s).

Preferably, a method of the present invention results in production ofmultipotent or pluripotent or totipotent cells, more preferably,pluripotent cells. In one example, the reprogrammed cells (i) express acell marker selected from the group consisting of Oct-4, SSEA3, SSEA4,Tra-1-60 and Tra-1-81; (ii) exhibit morphology characteristic ofpluripotent cells; and (iii) form teratomas when introduced into animmunocompromised animal.

In another example, the method of the present invention additionallycomprises differentiating the reprogrammed cells into a population ofcells comprising or enriched for a desired cell type. The method of theinvention may also comprise isolating, enriching or selecting for thedesired cell type. Such cells are useful in therapy or screening, e.g.,as described herein. Alternatively, such differentiated cells are usefulfor research into disease states or conditions, e.g., if the pluripotentcells are produced from a subject suffering from the condition.

In another example, the method of the present invention comprisesformulating an effective amount of a cell produced by a method describedherein according to any embodiment into a pharmaceutical compositionwith a pharmaceutically acceptable carrier or excipient.

In another example, the present invention provides a cell or populationthereof or a population enriched for reprogrammed cells produced by amethod as described herein according to any embodiment. Similarly,exemplary forms of the present invention provide a cell or population ofcells differentiated from the cell or population as described hereinaccording to any embodiment.

Another example of the present invention provides a Stro-1⁺multipotential cell and/or progeny cell thereof comprising a nucleicacid encoding a potency determining factor operably linked to aheterologous promoter. Such a cell is useful for producing areprogrammed cell.

Cells produced by performing a method as described herein according toany embodiment are useful in medicine, e.g., in a method of treating orpreventing a disease or disorder, the method comprising administeringthe cell or population thereof to a subject in need thereof.

Cells produced by performing a method as described herein according toany embodiment are also useful for screening. For example, thepresenting invention provides a method of screening for compounds usefulin the treatment or prevention of a disease or disorder, the methodcomprising exposing the cell or population according to the presentinvention to said compounds.

For example, the present invention also provides a method foridentifying a compound that directs differentiation of a pluripotentcell, the method comprising:

i) contacting a pluripotent cell produced according to the presentinvention or population thereof with a test compound and determining theamount of cells differentiated therefrom;ii) determining the amount of cells differentiated from a pluripotentcell produced according to the present invention or population thereofin the absence of the compound,wherein an increased amount of differentiated cells at (i) compared to(ii) indicates that the compound directs differentiation of apluripotent cell.

Preferably, the method comprises determining the amount of one or moredistinct differentiated cell types. In this manner, a compound thatdirects differentiation to a specific lineage or cell type isdetermined.

It will be apparent to the skilled artisan based on the foregoing thatthe present invention also provides a method for identifying a compoundthat reduces or prevents differentiation of a pluripotent cell.

The present invention also provides a method for identifying orisolating a compound useful for treating a condition, the methodcomprising:

(i) performing a method as described herein according to any embodimentto produce a pluripotent cell or population thereof from a subjectsuffering from the condition; and(ii) contacting the cell or population with a test compound anddetermining its effect on one or more symptoms of the condition, whereina compound that improves or alleviates a symptom of the condition isuseful for treating the condition.

In on example, the method comprises:

(a) differentiating the pluripotent cell or population thereof intocells affected in the condition; and(b) contacting the cells at (a) with the test compound and determiningits effect on one or more symptoms of the condition, wherein a compoundthat improves or alleviates a symptom of the condition is useful fortreating the condition.

Such a method is useful not only for identifying or isolating newcompounds for treating a condition, but also for identifying whether ornot a subject is likely to respond to treatment with an existingtherapeutic/prophylactic compound.

Such a method is further also useful for identifying any specific toxiceffects of a compound when that compound is exposed to one or moretarget tissues which are mature and differentiated and derived fromreprogrammed Stro-1⁺ multipotent cells and/or progeny cells thereof.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS General

Throughout this specification, unless specifically stated otherwise orthe context requires otherwise, reference to a single step, compositionof matter, group of steps or group of compositions of matter shall betaken to encompass one and a plurality (i.e. one or more) of thosesteps, compositions of matter, groups of steps or group of compositionsof matter.

Each embodiment described herein is to be applied mutatis mutandis toeach and every other embodiment unless specifically stated otherwise.

Those skilled in the art will appreciate that the invention describedherein is susceptible to variations and modifications other than thosespecifically described. It is to be understood that the inventionincludes all such variations and modifications. The invention alsoincludes all of the steps, features, compositions and compounds referredto or indicated in this specification, individually or collectively, andany and all combinations or any two or more of said steps or features.

The present invention is not to be limited in scope by the specificembodiments described herein, which are intended for the purpose ofexemplification only. Functionally-equivalent products, compositions andmethods are clearly within the scope of the invention, as describedherein.

The present invention is performed without undue experimentation using,unless otherwise indicated, conventional techniques of molecularbiology, microbiology, virology, recombinant DNA technology, peptidesynthesis in solution, solid phase peptide synthesis, and immunology.Such procedures are described, for example, in Sambrook, Fritsch &Maniatis, Molecular Cloning: A Laboratory Manual, Cold Spring HarborLaboratories, New York, Second Edition (1989), whole of VoIs I, II, andDI; DNA Cloning: A Practical Approach, Vols. I and II (D. N. Glover,ed., 1985), IRL Press, Oxford, whole of text; Oligonucleotide Synthesis:A Practical Approach (M. J. Gait, ed, 1984) IRL Press, Oxford, whole oftext, and particularly the papers therein by Gait, pp 1-22; Atkinson etal, pp 35-81; Sproat et al, pp 83-115; and Wu et al, pp 135-151; 4.Nucleic Acid Hybridization: A Practical Approach (B. D. Hames & S. J.Higgins, eds., 1985) IRL Press, Oxford, whole of text; Immobilized Cellsand Enzymes: A Practical Approach (1986) IRL Press, Oxford, whole oftext; Perbal, B., A Practical Guide to Molecular Cloning (1984); MethodsIn Enzymology (S. Colowick and N. Kaplan, eds., Academic Press, Inc.),whole of series; J. F. Ramalho Ortigao, “The Chemistry of PeptideSynthesis” In: Knowledge database of Access to Virtual Laboratorywebsite (Interactiva, Germany); Sakakibara, D., Teichman, J., Lien, E.Land Fenichel, R. L. (1976). Biochem. Biophys. Res. Commun. 73 336-342;Merrifield, R. B. (1963). J. Am. Chem. Soc. 85, 2149-2154; Barany, G.and Merrifield, R. B. (1979) in The Peptides (Gross, E. and Meienhofer,J. eds.), vol. 2, pp. 1-284, Academic Press, New York. 12. Wünsch, E.,ed. (1974) Synthese von Peptiden in Houben-Weyls Metoden der OrganischenChemie (Müler, E., ed.), vol. 15, 4th edn., Parts 1 and 2, Thieme,Stuttgart; Bodanszky, M. (1984) Principles of Peptide Synthesis,Springer-Verlag, Heidelberg; Bodanszky, M. & Bodanszky, A. (1984) ThePractice of Peptide Synthesis, Springer-Verlag, Heidelberg; Bodanszky,M. (1985) Int. I Peptide Protein Res. 25, 449-474; Handbook ofExperimental Immunology, VoIs. I-IV (D. M. Weir and C. C. Blackwell,eds., 1986, Blackwell Scientific Publications); and Animal Cell Culture:Practical Approach, Third Edition (John R. W. Masters, ed., 2000), ISBN0199637970, whole of text.

SELECTED DEFINITIONS

By “collectively” is meant that the invention encompasses any number orcombination of the recited proteins or markers or groups of proteins ormarkers, and that, notwithstanding that such numbers or combinations ofproteins or markers or claims may define such combinations orsub-combinations separately and divisibly from any other combination ofproteins or markers or groups of proteins or markers.

Throughout this specification, unless the context requires otherwise,the word “comprise”, or variations such as “comprises” or “comprising”,will be understood to imply the inclusion of a stated step or element orinteger or group of steps or elements or integers but not the exclusionof any other step or element or integer or group of elements orintegers.

As used herein the term “derived from” shall be taken to indicate that aspecified integer may be obtained from a particular source albeit notnecessarily directly from that source.

As used herein, the term “effective amount” shall be taken to mean asufficient quantity of reprogrammed cells or cells differentiatedtherefrom and/or progeny cells thereof to improve a physiologicalprocess or disease state or to prevent a disease state from occurring ina subject compared to the same process or state prior to administrationand/or compared to a subject to which the cells are not administered.

As used herein, the term “enriched” in the context of a cell populationshall be taken to mean that the number or percentage of reprogrammedcells or pluripotent cells is greater than the number or percentage in anaturally occurring cell population. For example, a population enrichedin reprogrammed or pluripotent cells is made up of at least about 0.02%of said cells, or at least about 0.05% of said cells or at least about0.1% of said cells or at least about 0.2% of said cells or at leastabout 0.5% of said cells or at least about 0.5% of said cells or atleast about 0.8% of said cells or at least about 1% of said cells or atleast about 2% of said cells or at least about 3% of said cells or atleast about 4% of said cells or at least about 5% of said cells or atleast about 10% of said cells or at least about 15% of said cells or atleast about 20% of said cells or at least about 25% of said cells or atleast about 30% of said cells or at least about 40% of said cells or atleast about 50% of said cells or at least about 60% of said cells or atleast about 70% of said cells or at least about 80% of said cells or atleast about 85% of said cells or at least about 90% of said cells or atleast about 95% of said cells or at least about 97% of said cells or atleast about 98% of said cells or at least about 99% of said cells.

The term “expose” and grammatical equivalents, e.g., “exposing” shall betaken to mean any process by which a cell is brought into sufficientproximity with a potency determining factor for that factor to exert abiological effect on the cell. This term shall contacting a cell with anucleic acid encoding the factor and/or expressing the factor in a cell.

By “individually” is meant that the invention encompasses the recitedproteins or markers or groups of proteins or markers separately, andthat, notwithstanding that individual proteins or markers or groups ofproteins or markers may not be separately listed herein the accompanyingclaims may define such protein or marker or groups of proteins ormarkers separately and divisibly from each other.

As used herein, the term “iPS cells” refer to cells that aresubstantially genetically identical to their respective differentiatedsomatic cell of origin (e.g., a Stro-1⁺ multipotential cell or progenycell thereof) and display characteristics similar to higher potencycells, such as ES cells. iPS cells exhibit morphological (i.e., roundshape, large nucleoli and scant cytoplasm) and growth properties (i.e.,doubling time; ES cells have a doubling time of about seventeen toeighteen hours) akin to ES cells. In addition, iPS cells preferablyexpress pluripotent cell-specific markers (e.g., Oct-4, SSEA-3, SSEA-4,Tra-1-60, Tra-1-81, but not SSEA-I). iPS cells, however, are notimmediately derived from embryos and can transiently or stably expressone or more copies of selected potency-determining factors at leastuntil they become pluripotent. As used herein, “not immediately derivedfrom embryos” means that the starting cell type for producing iPS cellsis a non-pluripotent Stro-1⁺ mutilpotential cell or non-pluripotentprogeny thereof obtained from a post-natal individual.

As used herein, the term “multipotent” shall be taken to mean that acell is capable of differentiating into a plurality of different typescells of one or two or three of the three germ layers (mesoderm,endoderm and ectoderm), preferably one or two of the germ layers.

As used herein, the term “pluripotent” shall be taken to mean that acell is capable of differentiating into cells of each of the three germlayers, i.e., endoderm, ectoderm and mesoderm. Pluripotent cells expressa variety of pluripotent cell-specific markers (e.g., one or more of thefollowing pluripotent cell-specific markers: S SEA-3, SSEA-4, TRA-1-60or TRA 1-81), have a cell morphology characteristic of undifferentiatedcells (i.e., compact colony, high nucleus to cytoplasm ratio andprominent nucleolus) and form teratomas when introduced into animmunocompromised animal, such as a SCID mouse. The teratomas typicallycontain cells or tissues characteristic of all three germ layers. One ofordinary skill in the art can assess these characteristics by usingtechniques commonly used in the art, see, e.g., Thomson et al, Science282:1145-1147 (1998). Pluripotent cells are capable of bothproliferation in cell culture and differentiation towards a variety oflineage-restricted cell populations that exhibit multipotent properties.Multipotent somatic cells are more differentiated relative topluripotent cells, but are not terminally differentiated. Pluripotentcells therefore have a higher potency than multipotent cells.

As used herein, the term “potency-determining factor” refers to afactor, such as a gene or other nucleic acid, a functional fragmentthereof, as well as an encoded factor, e.g., protein or functionalfragment thereof, or small molecule or antibody used to increase thepotency of a somatic cell, so that it becomes multipotent, pluripotentor totipotent. The potency-determining factors optionally can be presentonly transiently in the reprogrammed cells or, in the case of a nucleicacid can be maintained in a transcriptionally active or inactive statein the genome of the reprogrammed cells. Likewise, nucleic acidpotency-determining factors can be present in more than one copy in thereprogrammed cells, where the potency-determining factor can beintegrated in the cell's genome, can be extra-chromosomal or both.Exemplary potency determining factors include Oct4 (exemplary nucleotideand amino acid sequences are set out in Genbank Accession No. BC117435.1or NCBI Accession No. NM 002701), Sox2 (exemplary nucleotide and aminoacid sequences are set out in NCBI Accession No. NM_003106.2), Klf4(exemplary nucleotide and amino acid sequences are set out in NCBIAccession No. NM_004235.4), Nanog (exemplary nucleotide and amino acidsequences are set out in NCBI Accession No. NM 024865.2), Lin28(exemplary nucleotide and amino acid sequences are set out in NCBIAccession No. NM_024674.4), c-Myc (exemplary nucleotide and amino acidsequences are set out in Genbank Accession No. L16785.1, bFGF, SCF,TERT, SV40 large T antigen, HPV16E6, HPV16E7, Bmil, Fbx15, Eras,ECAT15-2, Tcl1, β-catenin, ECAT1, ESG1, Dnmt3L, ECAT8, Gdf3, Sox15,ECAT15-1, Fthl17, Sal14, Rex1 (exemplary sequences set out in NCBIAccession No. NM 174900), UTF1 (exemplary sequences set out in NCBIAccession No. NM 003577), Stella (exemplary sequences set out in NCBIaccession No. NM 199286), Stat3, FoxD3 (exemplary sequences set out inNCBI Accession no. NM 012183), ZNF206, Myb12, DPP A2, Otx2 and Grb2. AllAccession Numbers provided herein are current as at Feb. 20, 2009. Theskilled artisan will be readily able to determine the structure of otherpotency determining factors as described herein, e.g., using databasessuch as NCBI or GenBank. Compounds having the same or similar activityto said factors are also included. Such compounds include antibodies andsmall molecules capable with enhancing or inducing reprogramming, e.g.,a histone deacetylase inhibitor or a DNA methylase or inhibitor thereof.The skilled artisan will be capable of determining suitable compounds,e.g., using methods described herein in which one or more potencydetermining factors is omitted and a panel of test compounds assessedand/or using the cells and/or methods described in Markoulaki et alNature Biotechnology 27, 169-171 (2009).

As used herein, the term “potent” shall be taken to mean the ability ofa cell to differentiate into more than one cell type. Accordingly, acell with greater potency is capable of differentiating into more celltypes than a cell with less potency.

As used herein, the term “prophylactically effective amount” shall betaken to mean a sufficient quantity of reprogrammed cells or cellsdifferentiated therefrom and/or progeny cells thereof to prevent orinhibit the onset of or delay the onset of one or more detectablesymptoms of a clinical condition.

As used herein, the term “prevent” or “preventing” or “prevention” shallbe taken to mean administering a prophylactically effective amount ofcells and stopping or hindering or delaying or reducing the developmentof at least one symptom of a clinical condition.

As used herein, the term “reprogramming” refers to a process wherebysomatic cells are converted into de-differentiated and/ormultipotent/pluripotent/totipotent cells, and thus have a greaterpotency potential than the cells from which they were derived.Preferably, the reprogrammed cells are multipotent, pluripotent ortotipotent, and more preferably, pluripotent. The term “reprogrammed”refers to a somatic cell that has been de-differentiated to make itmultipotent/pluripotent/totipotent.

As used herein, the phrase “STRO-1⁺ multipotential cells” shall be takento mean non-hematopoietic STRO-1⁺ and/or TNAP⁺ progenitor cells capableof forming multipotential cell colonies. Preferred STRO-1⁺multipotential cells are discussed in more detail herein.

As used herein, the term “subject” shall be taken to mean any subjectcomprising Stro-1⁺ cells, preferably a mammal. Exemplary subjectsinclude but are not limited to human, primate, livestock (e.g. sheep,cow, horse, donkey, pig), companion animals (e.g. dogs, cats),laboratory test animals (e.g. mice, rabbits, rats, guinea pigs,hamsters), captive wild animal (e.g. fox, deer). Preferably the mammalis a human or primate. Most preferably the mammal is a human.

As used herein, the term “totipotent” shall be taken to mean that a cellis capable of differentiating into cells of each of the three germlayers and extraembryonic tissues.

As used herein, the term “therapeutically effective amount” shall betaken to mean a sufficient quantity of reprogrammed cells or cellsdifferentiated therefrom and/or progeny cells thereof to reduce orinhibit one or more symptoms of a clinical condition.

As used herein, the term “treat” or “treatment” or “treating” shall beunderstood to mean administering a therapeutically effective amount ofcells and reducing or inhibiting at least one symptom of a clinicalcondition.

STRO-1⁺ Multipotential Cells or Progeny Cells

STRO-1⁺ multipotential cells are cells found in bone marrow, blood,dental pulp cells, adipose tissue, skin, spleen, pancreas, brain,kidney, liver, heart, retina, brain, hair follicles, intestine, lung,lymph node, thymus, bone, ligament, tendon, skeletal muscle, dermis, andperiosteum; and are capable of differentiating into germ lines such asmesoderm and/or endoderm and/or ectoderm. Preferably, the STRO-1⁺ cellsare from bone marrow, dental pulp or adipose tissue, more preferablyfrom dental pulp or adipose tissue. Thus, STRO-1⁺ multipotential cellsare capable of differentiating into a large number of cell typesincluding, but not limited to, adipose, osseous, cartilaginous, elastic,muscular, and fibrous connective tissues. The specificlineage-commitment and differentiation pathway which these cells enterdepends upon various influences from mechanical influences and/orendogenous bioactive factors, such as growth factors, cytokines, and/orlocal microenvironmental conditions established by host tissues. STRO-1⁺multipotential cells are thus non-hematopoietic progenitor cells whichdivide to yield daughter cells that are either stem cells or areprecursor cells which in time will irreversibly differentiate to yield aphenotypic cell.

In a preferred embodiment, the STRO-1⁺ multipotential cells are enrichedfrom a sample obtained from a subject, e.g., a subject to be treated ora related subject or an unrelated subject (whether of the same speciesor different). Such an enrichment may be performed ex vivo or in vitroThe terms ‘enriched’, ‘enrichment’ or variations thereof are used hereinto describe a population of cells in which the proportion of oneparticular cell type or the proportion of a number of particular celltypes is increased when compared with the untreated population.

In a preferred embodiment, the cells used in the present inventionexpress one or more markers individually or collectively selected fromthe group consisting of TNAP⁺, VCAM-1⁺, THY-1⁺, STRO-2⁺, CD45⁺, CD146⁺,3G5⁺ or any combination thereof.

Preferably, the STRO-1⁺ cells are STRO-1^(bright) (syn. STRO-1^(bri)).Preferably, the STRO-1^(bright) cells are additionally one or more ofTNAP⁺, VCAM-1⁺, THY-1⁺, STRO-2⁺ and/or CD146⁺.

In one embodiment, the mesenchymal precursor cells are perivascularmesenchymal precursor cells as defined in WO 2004/85630.

A cell that is referred to as being “positive” for a given marker it mayexpress either a low (lo or dim) or a high (bright, bri) level of thatmarker depending on the degree to which the marker is present on thecell surface, where the terms relate to intensity of fluorescence orother marker used in the sorting process of the cells. The distinctionof lo (or dim or dull) and bri will be understood in the context of themarker used on a particular cell population being sorted. A cell that isreferred to as being “negative” for a given marker is not necessarilycompletely absent from that cell. This term means that the marker isexpressed at a relatively very low level by that cell, and that itgenerates a very low signal when detectably labelled or is undetectableabove background levels.

The term “bright”, when used herein, refers to a marker on a cellsurface that generates a relatively high signal when detectablylabelled. Whilst not wishing to be limited by theory, it is proposedthat “bright” cells express more of the target marker protein (forexample the antigen recognised by STRO-1) than other cells in thesample. For instance, STRO-1^(bri) cells produce a greater fluorescentsignal, when labelled with a FITC-conjugated STRO-1 antibody asdetermined by fluorescence activated cell sorting (FACS) analysis, thannon-bright cells (STRO-1^(dull/dim)). Preferably, “bright” cellsconstitute at least about 0.1% of the most brightly labelled bone marrowmononuclear cells contained in the starting sample. In otherembodiments, “bright” cells constitute at least about 0.1%, at leastabout 0.5%, at least about 1%, at least about 1.5%, or at least about2%, of the most brightly labelled bone marrow mononuclear cellscontained in the starting sample. In a preferred embodiment,STRO-1^(bright) cells have 2 log magnitude higher expression of STRO-1surface expression relative to “background”, namely cells that areSTRO-1⁻. By comparison, STRO-1^(dim) and/or STRO-1^(intermediate) cellshave less than 2 log magnitude higher expression of STRO-1 surfaceexpression, typically about 1 log or less than “background”.

As used herein the term “TNAP” is intended to encompass all isoforms oftissue non-specific alkaline phosphatase. For example, the termencompasses the liver isoform (LAP), the bone isoform (BAP) and thekidney isoform (KAP). In a preferred embodiment, the TNAP is BAP. In aparticularly preferred embodiment, TNAP as used herein refers to amolecule which can bind the STRO-3 antibody produced by the hybridomacell line deposited with ATCC on 19 Dec. 2005 under the provisions ofthe Budapest Treaty under deposit accession number PTA-7282.

Furthermore, in a preferred embodiment, the STRO-1⁺ multipotential cellsare capable of giving rise to clonogenic CFU-F.

It is preferred that a significant proportion of the multipotentialcells are capable of differentiation into at least two different germlines. Non-limiting examples of the lineages to which the multipotentialcells may be committed include bone precursor cells; hepatocyteprogenitors, which are multipotent for bile duct epithelial cells andhepatocytes; neural restricted cells, which can generate glial cellprecursors that progress to oligodendrocytes and astrocytes; neuronalprecursors that progress to neurons; precursors for cardiac muscle andcardiomyocytes, glucose-responsive insulin secreting pancreatic betacell lines. Other lineages include, but are not limited to,odontoblasts, dentin-producing cells and chondrocytes, and precursorcells of the following: retinal pigment epithelial cells, fibroblasts,skin cells such as keratinocytes, dendritic cells, hair follicle cells,renal duct epithelial cells, smooth and skeletal muscle cells,testicular progenitors, vascular endothelial cells, tendon, ligament,cartilage, adipocyte, fibroblast, marrow stroma, cardiac muscle, smoothmuscle, skeletal muscle, pericyte, vascular, epithelial, glial,neuronal, astrocyte and oligodendrocyte cells.

In another embodiment, the STRO-1⁺ multipotential cells are not capableof giving rise, upon culturing, to hematopoietic cells.

In one embodiment, the cells are taken from the subject to be treatedand cultured in vitro using standard techniques, e.g., prior to use in amethod as described herein according to any embodiment. Such cells orcells differentiated therefrom are useful for administration to thesubject in an autologous or allogeneic composition. In an alternativeembodiment, cells of one or more of the established human cell lines areused. In another useful embodiment of the invention, cells of anon-human animal (or if the patient is not a human, from anotherspecies) are used.

The progeny cells may be obtained by culturing in any suitable medium.The term “medium”, as used in reference to a cell culture, includes thecomponents of the environment surrounding the cells. Media may be solid,liquid, gaseous or a mixture of phases and materials. Media includeliquid growth media as well as liquid media that do not sustain cellgrowth. Media also include gelatinous media such as agar, agarose,gelatin and collagen matrices. Exemplary gaseous media include thegaseous phase that cells growing on a petri dish or other solid orsemisolid support are exposed to. The term “medium” also refers tomaterial that is intended for use in a cell culture, even if it has notyet been contacted with cells. In other words, a nutrient rich liquidprepared for bacterial culture is a medium. A powder mixture that whenmixed with water or other liquid becomes suitable for cell culture maybe termed a “powdered medium”.

In an embodiment, progeny cells useful for the methods of the inventionare obtained by isolating TNAP⁺ STRO-1⁺ multipotential cells from bonemarrow using magnetic beads labelled with the STRO-3 antibody, and thenculture expanding the isolated cells (see Gronthos et al. Blood 85:929-940, 1995 for an example of suitable culturing conditions).

In one embodiment, such expanded cells (progeny) (preferably, at leastafter 5 passages) can be TNAP⁻, CC9⁺, HLA class I⁺, HLA class II⁻,CD14⁻, CD19⁻, CD3⁻, CD11a⁻c⁻, CD31⁻, CD86⁻, CD34⁻ and/or CD80⁻. However,it is possible that under different culturing conditions to thosedescribed herein that the expression of different markers may vary.Also, whilst cells of these phenotypes may predominate in the expendedcell population it does not mean that there is a minor proportion of thecells do not have this phenotype(s) (for example, a small percentage ofthe expanded cells may be CC9⁻). In one preferred embodiment, expandedcells still have the capacity to differentiate into different celltypes.

In a further embodiment, the expanded cells may express one or moremarkers collectively or individually selected from the group consistingof LFA-3, THY-1, VCAM-1, ICAM-1, PECAM-1, P-selectin, L-selectin, 3G5,CD49a/CD49b/CD29, CD49c/CD29, CD49d/CD29, CD 90, CD29, CD18, CD61,integrin beta 6-19, thrombomodulin, CD10, CD13, SCF, PDGF-R, EGF-R,IGF1-R, NGF-R, FGF-R, Leptin-R (STRO-2=Leptin-R), RANKL, STRO-1^(bright)and CD146 or any combination of these markers.

In one embodiment, the progeny cells are Multipotential Expanded STRO-1⁺Multipotential cells Progeny (MEMPs) as defined and/or described in WO2006/032092. Methods for preparing enriched populations of STRO-1⁺multipotential cells from which progeny may be derived are described inWO 01/04268 and WO 2004/085630. In an in vitro context STRO-1⁺multipotential cells will rarely be present as an absolutely purepreparation and will generally be present with other cells that aretissue specific committed cells (TSCCs). WO 01/04268 refers toharvesting such cells from bone marrow at purity levels of about 0.1% to90%. The population comprising mutilpotential cells from which progenyare derived may be directly harvested from a tissue source, oralternatively it may be a population that has already been expanded exvivo.

For example, the progeny may be obtained from a harvested, unexpanded,population of substantially purified STRO-1⁺ multipotential cells,comprising at least about 0.1, 1, 5, 10, 20, 30, 40, 50, 60, 70, 80 or95% of total cells of the population in which they are present. Thislevel may be achieved, for example, by selecting for cells groupconsisting of TNAP, STRO-1^(bright), 3G5⁺, VCAM-1, THY-1, CD146 andSTRO-2.

MEWS can be distinguished from freshly harvested STRO-1⁺ multipotentialcells in that they are positive for the marker STRO-1^(bri) and negativefor the marker Alkaline phosphatase (ALP). In contrast, freshly isolatedSTRO-1⁺ multipotential cells are positive for both STRO-1^(bri) and ALP.In a preferred embodiment of the present invention, at least 15%, 20%,30%, 40%, 50%, 60%, 70%, 80%, 90% or 95% of the administered cells havethe phenotype STRO-1^(bri), ALP⁻. In a further preferred embodiment theMEMPS are positive for one or more of the markers Ki67, CD44 and/orCD49c/CD29, VLA-3, α3β1. In yet a further preferred embodiment the MEMPsdo not exhibit TERT activity and/or are negative for the marker CD18.

The STRO-1⁺ multipotential cell starting population may be derived fromany one or more tissue types set out in WO 01/04268 or WO 2004/085630,namely bone marrow, dental pulp cells, adipose tissue and skin, orperhaps more broadly from adipose tissue, teeth, dental pulp, skin,liver, kidney, heart, retina, brain, hair follicles, intestine, lung,spleen, lymph node, thymus, pancreas, bone, ligament, bone marrow,tendon and skeletal muscle.

It will be understood that in performing the present invention,separation of cells carrying any given cell surface marker can beeffected by a number of different methods, however, preferred methodsrely upon binding a binding agent (e.g., an antibody or antigen bindingfragment thereof) to the marker concerned followed by a separation ofthose that exhibit binding, being either high level binding, or lowlevel binding or no binding. The most convenient binding agents areantibodies or antibody-based molecules, preferably being monoclonalantibodies or based on monoclonal antibodies because of the specificityof these latter agents. Antibodies can be used for both steps, howeverother agents might also be used, thus ligands for these markers may alsobe employed to enrich for cells carrying them, or lacking them.

The antibodies or ligands may be attached to a solid support to allowfor a crude separation. The separation techniques preferably maximisethe retention of viability of the fraction to be collected. Varioustechniques of different efficacy may be employed to obtain relativelycrude separations. The particular technique employed will depend uponefficiency of separation, associated cytotoxicity, ease and speed ofperformance, and necessity for sophisticated equipment and/or technicalskill. Procedures for separation may include, but are not limited to,magnetic separation, using antibody-coated magnetic beads, affinitychromatography and “panning” with antibody attached to a solid matrix.Techniques providing accurate separation include but are not limited toFACS. Methods for performing FACS will be apparent to the skilledartisan.

Antibodies against each of the markers described herein are commerciallyavailable (e.g., monoclonal antibodies against STRO-1 are commerciallyavailable from R&D Systems, USA), available from ATCC or otherdepositary organization and/or can be produced using art recognizedtechniques.

It is preferred that the method for isolating STRO-1⁺ multipotentialcells, for example, comprises a first step being a solid phase sortingstep utilising for example magnetic activated cell sorting (MACS)recognising high level expression of STRO-1. A second sorting step canthen follow, should that be desired, to result in a higher level ofprecursor cell expression as described in patent specification WO01/14268. This second sorting step might involve the use of two or moremarkers.

The method obtaining STRO-1⁺ multipotential cells might also include theharvesting of a source of the cells before the first enrichment stepusing known techniques. Thus the tissue will be surgically removed.Cells comprising the source tissue will then be separated into a socalled single cells suspension. This separation may be achieved byphysical and or enzymatic means.

Once a suitable STRO-1⁺ multipotential cell population has beenobtained, it may be cultured or expanded by any suitable means to obtainMEMPs.

The invention can be practised using cells from any non-human animalspecies, including but not limited to non-human primate cells, ungulate,canine, feline, lagomorph, rodent, avian, and fish cells. Primate cellswith which the invention may be performed include but are not limited tocells of chimpanzees, baboons, cynomolgus monkeys, and any other New orOld World monkeys. Ungulate cells with which the invention may beperformed include but are not limited to cells of bovines, porcines,ovines, caprines, equines, buffalo and bison. Rodent cells with whichthe invention may be performed include but are not limited to mouse,rat, guinea pig, hamster and gerbil cells. Examples of lagomorph specieswith which the invention may be performed include domesticated rabbits,jack rabbits, hares, cottontails, snowshoe rabbits, and pikas. Chickens(Gallus gallus) are an example of an avian species with which theinvention may be performed.

Cells useful for the methods of the invention may be stored before use,or before obtaining the supernatant or soluble factors. Methods andprotocols for preserving and storing of eukaryotic cells, and inparticular mammalian cells, are known in the art (cf., for example,Pollard, J. W. and Walker, J. M. (1997) Basic Cell Culture Protocols,Second Edition, Humana Press, Totowa, N.J.; Freshney, R. I. (2000)Culture of Animal Cells, Fourth Edition, Wiley-Liss, Hoboken, N.J.). Anymethod maintaining the biological activity of the isolated stem cellssuch as mesenchymal stem/progenitor cells, or progeny thereof, may beutilized in connection with the present invention. In one preferredembodiment, the cells are maintained and stored by usingcryo-preservation.

Genetically-Modifying Cells to Express Potency-Determining Factors

In one embodiment, the STRO-1⁺ multipotential cells and/or progeny cellsthereof are genetically modified, e.g., to express a potency determiningfactor or plurality thereof.

Methods for genetically modifying a cell will be apparent to the skilledartisan. For example, a nucleic acid that is to be expressed in a cellis operably-linked to a promoter for inducing expression in the cell andpreferably in a plurlipotent cell. For example, the nucleic acid isoperably-linked to a promoter operable in a variety of cells of asubject, such as, for example, a viral promoter, e.g., a CMV promoter(e.g., a CMV-IE promoter) or a SV-40 promoter, or an elongation factorpromoter or an inducible promoter, e.g., a tet-inducible promoter.Additional suitable promoters are known in the art and shall be taken toapply mutatis mutandis to the present embodiment of the invention. Thepresent invention also encompasses the use of a multicistronic vector topermit expression of a plurality of potency-determining factors from asingle promoter, e.g., Oct4 and Sox2. Such vectors generally comprise aninternal ribosome entry site (IRES) separating two nucleic acids eachencoding different potency determining factors.

As used herein, the term “promoter” is to be taken in its broadestcontext and includes the transcriptional regulatory sequences of agenomic gene, including the TATA box or initiator element, which isrequired for transcription initiation, with or without additionalregulatory elements (i.e., upstream activating sequences, transcriptionfactor binding sites, enhancers and silencers) which alter geneexpression, e.g., in response to developmental and/or external stimuli,or in a tissue specific manner. In the present context, the term“promoter” is also used to describe a recombinant, synthetic or fusionmolecule, or derivative which confers, activates or enhances theexpression of a nucleic acid to which it is operably-linked, andpreferably which encodes a peptide or protein. Preferred promoters cancontain additional copies of one or more specific regulatory elements tofurther enhance expression and/or alter the spatial expression and/ortemporal expression of said nucleic acid molecule.

In the present context, a nucleic acid is “operably-linked” with or to apromoter (i.e., under the regulatory control of a promoter) when it ispositioned such that its expression is controlled by the promoter.Promoters are generally positioned 5′ (upstream) to the nucleic acid,the expression of which they control. To construct heterologouspromoter/nucleic acid combinations, it is generally preferred toposition the promoter at a distance from the gene transcription startsite that is approximately the same as the distance between thatpromoter and the gene it controls in its natural setting, i.e., the genefrom which the promoter is derived. As is known in the art, somevariation in this distance can be accommodated without loss of promoterfunction. Similarly, the preferred positioning of a regulatory sequenceelement with respect to a heterologous nucleic acid to be placed underits control is defined by the positioning of the element in its naturalsetting, i.e., the gene from which it is derived. Again, as is known inthe art, some variation in this distance can also occur.

Preferably, the nucleic acid is provided in the form of an expressionconstruct. As used herein, the term “expression construct” refers to anucleic acid that has the ability to confer expression on a nucleic acidto which it is operably-linked, in a cell. Within the context of thepresent invention, it is to be understood that an expression constructmay comprise or be a plasmid, bacteriophage, phagemid, cosmid, virussub-genomic or genomic fragment, or other nucleic acid capable ofconferring expression on heterologous DNA. The expression construct canintegrate into the genome of a cell or remain episomal.

Preferred expression constructs are capable of remaining episomal, e.g.,plasmids and phagemids. Such expression constructs are useful, forexample, for producing reprogrammed cells in which an expressionconstruct has not been integrated into the genome. Moreover, becausethese expression constructs are often lost during cell division, it ispossible to produce reprogrammed cells that do not comprise therecombinant expression construct (see, for example, Okita et al.,Science, 322:949-53, 2008.

Methods for the construction of a suitable expression construct forperformance of the invention will be apparent to the skilled artisan andare described, for example, in Ausubel et al (In: Current Protocols inMolecular Biology. Wiley Interscience, ISBN 047 150338, 1987) orSambrook et al (In: Molecular Cloning: Molecular Cloning: A LaboratoryManual, Cold Spring Harbor Laboratories, New York, Third Edition 2001).For example, each of the components of the expression construct isamplified from a suitable template nucleic acid using, for example, PCRand subsequently cloned into a suitable expression construct, such asfor example, a plasmid or a phagemid.

Vectors suitable for such an expression construct are known in the artand/or described herein. For example, an expression vector suitable forthe method of the present invention in a mammalian cell is, for example,a vector of the pcDNA vector suite supplied by Invitrogen, a vector ofthe pCI vector suite (Promega), a vector of the pCMV vector suite(Clontech), a pM vector (Clontech), a pSI vector (Promega), a VP 16vector (Clontech) or a vector of the pcDNA vector suite (Invitrogen).

The skilled artisan will be aware of additional vectors and sources ofsuch vectors, such as, for example, Invitrogen Corporation, Clontech orPromega.

Means for introducing the isolated nucleic acid molecule or a geneconstruct comprising same into a cell for expression are known to thoseskilled in the art. The technique used for a given organism depends onthe known successful techniques. Means for introducing recombinant DNAinto cells include calcium phosphate precipitation (Graham and Van DerEb, Virology, 52: 456-467,1973; Chen and Okayama, Mol. Cell Biol., 7:2745-2752, 1987; Rippe et al., Mol. Cell Biol., 10: 689-695, 1990)DEAE-dextran (Gopal, Mol. Cell Biol., 5: 1188-1190, 1985),electroporation (Tur-Kaspa et al., Mol. Cell Biol., 6: 716-718, 1986;Potter et al., Proc. Natl Acad. Sci. USA, 81: 7161-7165, 1984), directmicroinjection, DNA-loaded liposomes (Nicolau and Sene, Biochim.Biophys. Acta, 721: 185-190, 1982; Fraley et al., Proc. Natl Acad. Sci.USA, 76: 3348-3352, 1979), cell sonication (Fechheimer et al., Proc.Natl Acad. Sci. USA, 84: 8463-8467, 1987), gene bombardment using highvelocity microprojectiles (Yang et al., Proc. Natl Acad. Sci USA, 87:9568-9572, 1990), receptor-mediated transfection (Wu and Wu, J. Biol.Chem., 262: 4429-4432, 19877; Wu and Wu, Biochem., 27: 887-892, 1988).In other embodiments, transfer of nucleic acids into cells may beaccomplished by formulating the nucleic acids with nanocaps (e.g.,nanoparticulate CaP04), colloidal gold, nanoparticulate syntheticpolymers, and/or liposomes.

In one preferred embodiment, an expression construct that remainsepisomal or does not otherwise integrate into the genome of a cell istransfected, e.g., using a method described above or in Okita et al,2008, supra. Preferably, the plasmid is repeatedly transfected into saidcell until said cell is reprogrammed. In this manner, a cell that doesnot have heterologous DNA integrated into its genome is produced, whichis more attractive from a therapeutic point of view.

Alternatively, an expression construct of the invention is a viralvector. Suitable viral vectors are known in the art and commerciallyavailable. Conventional viral-based systems for the delivery of anucleic acid and integration of that nucleic acid into a host cellgenome include, for example, a retroviral vector, a lentiviral vector oran adeno-associated viral vector. Alternatively, an adenoviral vector isuseful for introducing a nucleic acid that remains episomal into a hostcell, e.g., to produce a reprogrammed cell that does not includeheterologous DNA integrated into its genome. Viral vectors are anefficient and versatile method of gene transfer in target cells andtissues. Additionally, high transduction efficiencies have been observedin many different cell types and target tissues. Exemplary viral vectorsare discussed below.

a) Adenoviral Vectors

In one example, a viral gene delivery system useful in the presentinvention utilizes adenovirus-derived vectors. Knowledge of the geneticorganization of adenovirus, a 36 kB, linear and double-stranded DNAvirus, allows substitution of a large piece of adenoviral DNA withforeign sequences up to 8 kB. The infection of adenoviral DNA into hostcells does not result in chromosomal integration because adenoviral DNAcan replicate in an episomal manner without potential genotoxicity.Also, adenoviruses are structurally stable, and no genome rearrangementhas been detected after extensive amplification. Adenovirus can infectvirtually all epithelial cells regardless of their cell cycle stage.Recombinant adenovirus is capable of transducing both dividing andnon-dividing cells. The ability to effectively transduce non-dividingcells makes adenovirus a good candidate for gene transfer into muscle orfat cells.

Adenovirus is particularly suitable for use as a gene transfer vectorbecause of its mid-sized genome, ease of manipulation, high titer, widetarget-cell range, and high infectivity. Both ends of the viral genomecontain 100-200 base pair (bp) inverted terminal repeats (ITR), whichare cis elements necessary for viral DNA replication and packaging.

The early (E) and late (L) regions of the genome contain differenttranscription units that are divided by the onset of viral DNAreplication. The E1 region (E1A and E1B) encodes proteins responsiblefor the regulation of transcription of the viral genome and a fewcellular genes. The expression of the E2 region (E2A and E2B) results inthe synthesis of the proteins for viral DNA replication. These proteinsare involved in DNA replication, late gene expression, and host cellshut off (Renan (1990) Radiotherap. Oncol. 19: 197). The products of thelate genes, including the majority of the viral capsid proteins, areexpressed only after significant processing of a single primarytranscript issued by the major late promoter (MLP). The MLP (located at16.8 from this promoter possess a 5′tripartite leader (TL) sequencewhich makes them exemplary mRNAs for translation.

The genome of an adenovirus can be manipulated such that it encodes agene product of interest, but is inactivated in terms of its ability toreplicate in a normal lytic viral life cycle (see, for example, Berkneret al., (1988) BioTechniques 6: 616; Rosenfeld et al., (1991) Science252: 431-434; and Rosenfeld et al., (1992) Cell 68: 143-155). Suitableadenoviral vectors derived from the adenovirus strain Ad type 5 d1324 orother strains of adenovirus (e. g., Ad2, Ad3, Ad7 etc.) are known tothose skilled in the art.

Recombinant adenoviruses can be advantageous in certain circumstances inthat they are capable of infecting nondividing cells and can be used toinfect a wide variety of cell types, including airway epithelium(Rosenfeld et al., (1992) cited supra), endothelial cells (Lemarchand etal., (1992) PNAS USA 89: 6482-6486), hepatocytes (Herz and Gerard,(1993) PNAS USA 90: 2812-2816) and muscle cells (Quantin et al., (1992)PNAS USA 89: 2581-2584; Ragot et al. (1993) Nature 361: 647).

Furthermore, the virus particle is relatively stable and amenable topurification and concentration, and can be modified so as to affect thespectrum of infectivity.

Moreover, the carrying capacity of the adenoviral genome for foreign DNAis large (up to 8 kilobases) relative to other gene delivery vectors(Berkner et al., supra; Haj-Ahmand and Graham (1986) J. Virol. 57: 267).Most replication-defective adenoviral vectors currently in use andtherefore favored by the present invention are deleted for all or partsof the viral E1 and E3 genes but retain as much as 80% of the adenoviralgenetic material (see, e. g., Jones et al., (1979) Cell 16: 683; Berkneret al., supra; and Graham et al., in Methods in Molecular Biology, E. J.Murray, Ed. (Humana, Clifton, N.J., 1991) vol. 7. pp. 109-127).Expression of the inserted polynucleotide of the invention can be undercontrol of, for example, the E1 A promoter, the major late promoter(MLP) and associated leader sequences, the viral E3 promoter, orexogenously added promoter sequences.

In certain embodiments, the adenovirus vector may be replicationdefective, or conditionally defective. The adenovirus may be of any ofthe 42 different known serotypes or subgroups A-F. Adenovirus type 5 ofsubgroup C is the exemplary starting material in order to obtain theconditional replication-defective adenovirus vector for use inaccordance with the methods and compositions described herein. This isbecause Adenovirus type 5 is a human adenovirus about which a great dealof biochemical and genetic information is known, and it has historicallybeen used for most constructions employing adenovirus as a vector. Asstated above, the typical vector according to the present invention isreplication defective and will not have an adenovirus E1 region. Thus,it will be most convenient to introduce the nucleic acid of interest atthe position from which the E1 coding sequences have been removed.However, the position of insertion of the polynucleotide in a regionwithin the adenovirus sequences is not critical to the presentinvention. For example, it may also be inserted in lieu of the deletedE3 region in E3 replacement vectors as described previously by Karlssonet. al. (1986) or in the E4 region where a helper cell line or helpervirus complements the E4 defect.

An exemplary helper cell line is 293 (ATCC Accession No. CRL1573). Thishelper cell line, also termed a “packaging cell line” was developed byFrank Graham (Graham et al. (1987) J. Gen. Virol. 36: 59-72 and Graham(1977) J. General Virology 68: 937-940) and provides E1A and E1B intrans. However, helper cell lines may also be derived from human cells,such as human embryonic kidney cells, muscle cells, hematopoietic cellsor other human embryonic mesenchymal or epithelial cells. Alternatively,the helper cells may be derived from the cells of other mammalianspecies that are permissive for human adenovirus. Such cells include, e.g., Vero cells or other monkey embryonic mesenchymal or epithelialcells.

Adenoviruses can also be cell type specific, i.e., infect onlyrestricted types of cells and/or express a desired nucleotide sequenceonly in restricted types of cells. For example, the viruses may comprisea gene under the transcriptional control of a transcription initiationregion specifically regulated by target host cells, as described e. g.,in U.S. Pat. No. 5,698,443. Thus, expression from replication competentadenoviruses can be restricted to certain cells by, e. g., inserting acell specific response element to regulate synthesis of a proteinnecessary for replication, e. g., E1A or E1B.

For additional detailed guidance on adenovirus technology which may beuseful in the practice of the subject invention, including methods andmaterials for the incorporation of a nucleic acid, propagation andpurification of recombinant virus containing the nucleic acid, and itsuse in transfecting cells and mammals, see also Wilson et al, WO94/28938, WO 96/13597 and WO 96/26285, and references cited therein.

b) Retroviruses

In certain embodiments, retroviral vectors may be used in accordancewith the methods and compositions described herein. Such viruses havebeen used to produce reprogrammed cells previously, albeit not inStro-1⁺ cells. The retroviruses are a group of single-stranded RNAviruses characterized by an ability to convert their RNA todouble-stranded DNA in infected cells by a process ofreverse-transcription (Coffin (1990) Retroviriae and their Replication”In Fields, Knipe ed. Virology. New York: Raven Press). The resulting DNAthen stably integrates into cellular chromosomes as a provirus anddirects synthesis of viral proteins. The integration results in theretention of the viral gene sequences in the recipient cell and itsdescendants. The retroviral genome contains three genes, gag, pol, andenv that code for capsid proteins, polymerase enzyme, and envelopecomponents, respectively. A sequence found upstream from the gag gene,termed psi, functions as a signal for packaging of the genome intovirions. Two long terminal repeat (LTR) sequences are present at the 5′and 3′ends of the viral genome. These contain strong promoter andenhancer sequences and are also required for integration in the hostcell genome (Coffin (1990), supra).

In order to construct a retroviral vector, a nucleic acid of interest isinserted into the viral genome in the place of certain viral sequencesto produce a virus that is replication-defective. In order to producevirions, a packaging cell line containing the gag, pol, and env genesbut without the LTR and psi components is constructed (Mann et al.(1983) Cell 33: 153). When a recombinant plasmid containing a nucleicacid of the invention, together with the retroviral LTR and psisequences is introduced into this cell line (by calcium phosphateprecipitation for example), the psi sequence allows the RNA transcriptof the recombinant plasmid to be packaged into viral particles, whichare then secreted into culture media (Nicolas and Rubenstein (1988)“Retroviral Vectors”, In: Rodriguez and Denhardt ed. Vectors: A Surveyof Molecular Cloning Vectors and their Uses. Stoneham, Butterworth, andTemin, (1986)“Retrovirus Vectors for Gene Transfer: EfficientIntegration into and Expression of Exogenous DNA in Vertebrate CellGenome”, In: Kucherlapati ed. Gene Transfer. New York: Plenum Press;Mann et al., 1983, supra). The media containing the recombinantretroviruses is then collected, optionally concentrated, and used forgene transfer. Retroviral vectors are able to infect a broad variety ofcell types.

The development of specialized cell lines (termed “packaging cells”)which produce only replication-defective retroviruses has increased theutility of retroviruses for gene therapy, and defective retroviruses arecharacterized for use in gene transfer for gene therapy purposes (for areview see Miller, A. D. (1990) Blood 76: 271). Thus, recombinantretrovirus can be constructed in which part of the retroviral codingsequence (gag, pol, env) has been replaced by nucleic acid encoding apeptide or analog of the present invention, e. g., a transcriptionalactivator, rendering the retrovirus replication defective. Thereplication defective retrovirus is then packaged into virions which canbe used to infect a target cell through the use of a helper virus bystandard techniques. Protocols for producing recombinant retrovirusesand for infecting cells in vitro or in vivo with such viruses can befound in Current Protocols in Molecular Biology, Ausubel, F. M. et al.,(eds.) Greene Publishing Associates, (1989), Sections 9.10-9. 14 andother standard laboratory manuals.

Examples of suitable retroviruses include pLJ, pZIP, pWE and pEM whichare known to those skilled in the art. An exemplary retroviral vector isa pSR MSVtkNeo (Muller et al. (1991) Mol. Cell Biol. 11: 1785 and pSRMSV (XbaI) (Sawyers et al. (1995) J. Exp. Med. 181: 307) and derivativesthereof. For example, the unique BamHI sites in both of these vectorscan be removed by digesting the vectors with BamHI, filling in withKlenow and religating to produce pSMTN2 and pSMTX2, respectively, asdescribed in WO 96/41865 by Clackson et al. Examples of suitablepackaging virus lines for preparing both ecotropic and amphotropicretroviral systems include Crip and Cre.

Retroviruses, including lentiviruses, have been used to introduce avariety of genes into many different cell types, including neural cells,epithelial cells, retinal cells, endothelial cells, lymphocytes,myoblasts, hepatocytes, bone marrow cells, in vitro and/or in vivo (seefor example, review by Federico (1999) Curr. Opin. Biotechnol. 10: 448;Eglitis et al., (1985) Science 230: 1395-1398; Danos and Mulligan,(1988) PNAS USA 85: 6460-6464; Wilson et al., (1988) PNAS USA 85:3014-3018; Armentano et al., (1990) PNAS USA 87: 6141-6145; Huber etal., (1991) PNAS USA 88: 8039-8043; Ferry et al., (1991) PNAS USA 88:8377-8381; Chowdhury et al., (1991) Science 254: 1802-1805; Kay et al.,(1992) Human Gene Therapy 3: 641-647; Dai et al., (1992) PNAS USA 89:10892-10895; Hwu et al., (1993) J. Immunol. 150: 4104-4115; U.S. Pat.No. 4,868,116; U.S. Pat. No. 4,980,286; PCT Application WO 89/07136; PCTApplication WO 89/02468; PCT Application WO 89/05345; and PCTApplication WO 92/07573).

Furthermore, it has been shown that it is possible to limit theinfection spectrum of retroviruses and consequently of retroviral-basedvectors, by modifying the viral packaging proteins on the surface of theviral particle (see, for example PCT publications WO 93/25234, WO94/06920, and WO 94/11524). For instance, strategies for themodification of the infection spectrum of retroviral vectors includecoupling antibodies specific for cell surface antigens to the viral envprotein (Roux et al., (1989) PNAS USA 86: 9079-9083; Julan et al.,(1992) J. Gen Virol 73: 3251-3255; and Goud et al., (1983) Virology 163:251-254); or coupling cell surface ligands to the viral env proteins(Neda et al., (1991) J. Biol. Chem. 266: 14143-14146). Coupling can bein the form of the chemical cross-linking with a protein or othervariety (e. g. lactose to convert the env protein to anasialoglycoprotein), as well as by generating fusion proteins (e. g.single-chain antibody/env fusion proteins).

c) Adeno-Associated Vectors

An exemplary viral vector system useful for delivery of a nucleic acidof the present invention is an adeno-associated virus (AAV). Humanadenoviruses are double-stranded DNA viruses which enter cells byreceptor-mediated endocytosis. These viruses have been considered wellsuited for gene transfer because they are easy to grow and manipulateand they exhibit a broad host range in vivo and in vitro. Adenovirusesare able to infect quiescent as well as replicating target cells andpersist extrachromosomally, rather than integrating into the hostgenome. AAV is a helper-dependent DNA parvovirus which belongs to thegenus Dependovirus. AAV has no known pathologies and is incapable ofreplication without additional helper functions provided by anothervirus, such as an adenovirus, vaccinia or a herpes virus, for efficientreplication and a productive life cycle.

In the absence of the helper virus, AAV establishes a latent state byinsertion of its genome into a host cell chromosome. Subsequentinfection by a helper virus rescues the integrated copy which can thenreplicate to produce infectious viral progeny. The combination of thewild type AAV virus and the helper functions from either adenovirus orherpes virus generates a recombinant AVV (rAVV) that is capable ofreplication. One advantage of this system is its relative safety (For areview, see Xiao et al., (1997) Exp. Neurol. 144: 113-124).

The AAV genome is composed of a linear, single-stranded DNA moleculewhich contains approximately 4681 bases (Berns and Bohenzky, (1987)Advances in Virus Research (Academic Press, Inc.) 32: 243-307). Thegenome includes inverted terminal repeats (ITRs) at each end whichfunction in cis as origins of DNA replication and as packaging signalsfor the virus. The internal nonrepeated portion of the genome includestwo large open reading frames, known as the AAV rep and cap regions,respectively. These regions code for the viral proteins involved inreplication and packaging of the virion. For a detailed description ofthe AAV genome, see, e. g., Muzyczka, N. (1992) Current Topics inMicrobiol. and Immunol. 158: 97-129.

Vectors containing as little as 300 base pairs of AAV can be packagedand can integrate. Space for exogenous DNA is limited to about 4.7 kb,which is sufficient to incorporate a nucleic acid encoding a peptide oranalog of the present invention. An AAV vector such as that described inTratschin et al., (1985) Mol. Cell. Biol. 5: 3251-3260 can be used tointroduce DNA into cells. A variety of nucleic acids have beenintroduced into different cell types using AAV vectors (see for exampleHermonat et al., (1984) PNAS USA 81: 6466-6470; Tratschin et al., (1985)Mol. Cell. Biol. 4: 2072-2081; Wondisford et al., (1988) Mol.Endocrinol. 2: 32-39; Tratschin et al., (1984) J. Virol. 51: 611-619;and Flotte et al., (1993) J. Biol. Chem. 268: 3781-3790).

General methods for the construction and delivery of rAAV constructs areknown in the art and described, for example, in Barlett, J. S., et al.,(1996), Protocols for Gene Transfer in Neuroscience; Towards GeneTherapy of Neurological Disorders, pp. 115-127.

The AAV-based expression vector to be used typically includes the 145nucleotide AAV inverted terminal repeats (ITRs) flanking a restrictionsite that can be used for subcloning of a desired nucleotide sequence,either directly using the restriction site available, or by excision ofthe desired nucleotide sequence with restriction enzymes followed byblunting of the ends, ligation of appropriate DNA linkers, restrictiondigestion, and ligation into the site between the ITRs.

For additional detailed guidance on AAV technology which may be usefulin the practice of the subject invention, including methods andmaterials for the incorporation of a nucleotide sequence, thepropagation and purification of the recombinant AAV vector containingthe nucleotide sequence, and its use in transfecting cells and mammals,see e. g., Carter et al, U.S. Pat. No. 4,797,368 (10 Jan. 1989);Muzyczka et al, U.S. Pat. No. 5,139,941 (18 Aug. 1992); Lebkowski et al,U.S. Pat. No. 5,173,414 (22 Dec. 1992); Srivastava, U.S. Pat. No.5,252,479 (12 Oct. 1993); Lebkowski et al, U.S. Pat. No. 5,354,678 (11Oct. 1994); Shenk et al, U.S. Pat. No. 5,436,146 (25 Jul. 1995);Chatterjee et al, U.S. Pat. No. 5,454,935 (12 Dec. 1995), Carter et alWO 93/24641 (published 9 Dec. 1993), and Natsoulis, U.S. Pat. No.5,622,856 (Apr. 22, 1997).

d) Other Viral Systems

Other viral vector systems that can be used to deliver nucleic acid maybe derived from, for example, herpes virus, e. g., Herpes Simplex Virus(IJ St U.S. Pat. No. 5,631,236 by Woo et al., issued May 20, 1997 and WO00/08191 by Neurovex), vaccinia virus (Ridgeway (1988) Ridgeway,“Mammalian expression vectors, “In: Rodriguez R L, Denhardt D T, ed.Vectors: A survey of molecular cloning vectors and their uses. Stoneham:Butterworth; Baichwal and Sugden (1986)” Vectors for gene transferderived from animal DNA viruses: Transient and stable expression oftransferred genes,” In: Kucherlapati R, ed. Gene transfer. New York:Plenum Press; Coupar et al. (1988) Gene, 68: 1-10), and several RNAviruses. Exemplary viruses include, for example, an alphavirus, apoxivirus, a vaccinia virus, a polio virus, and the like. They offerseveral attractive features for various mammalian cells (Friedmann(1989) Science, 244: 1275-1281; Ridgeway, 1988, supra; Baichwal andSugden, 1986, supra; Coupar et al., 1988; Horwich et al. (1990) J.Virol., 64: 642-650).

e) Non-Integrating Virus, Self-cleaving/Excisable Constructs and DirectTransfection of Plasmid to Target Somatic Cells

Expression of all genetic potency determining factors simultaneouslyfrom polycistronic expression cassettes, incorporating ‘self-cleaving’2A peptides, causes ‘ribosomal skipping’ to enable comparable expressionof each factor from a single promoter (Sommer et al., Stem Cells. 27:543-549, 2008; Carey et al., Proc. Natl. Acad. Sci. USA 106: 157-162,2009). With an internal ribosome entry sequence (IRES) separating pairsof factors, infected cells are capable of expressing all potentcydetermining factors or a subset thereof. Carey et al., (2009, supra)constructed doxycycline-inducible factors separated by self-cleaving 2Apeptides, without IRES technology.

In another example, one or more potency determining factors is deliveredusing a DNA transposon. DNA transposons are genetic elements that areexcised and re-integrated throughout the genome by specific‘transposase’ enzymes, a phenomenon referred to a transposition.piggyBac is one such transposon capable of harboring a multiple-genepayload that preferentially inserts in transcriptional DNA unitsharboring TTAA sequences. Induction of individual or polycistronic,doxycycline-inducible constructs, delivered to murine and humanfibroblasts by transposase-mediated integration and subsequent excision,generates iPS cells exhibiting all the hallmarks of pluripotency,including contribution to mid-gestation embryos by tetraploidcomplementation assay (Woltjen et al., Nature. 458: 766-770, 2009).

Additionally, foxed proviral constructs can be excised throughsubsequent infection with transient Cre-recombinase expressingadenovirus (Kaji et al., Nature. 458: 771-775, 2009).

Non-DNA-Based Methods for iPS Generation a) Chemical Approaches

In one example, a potency determining factor is an inhibitor of histonemethyltransferase G9a is used in place as or as a supplement to (e.g.,to reduced the level of expression of) Oct4. Chemical inhibition of G9acan be achieved with BIX-01294 (BIX), e.g., from Enzo Lifesciences, andhas been eases the antagonism on histone 3, lysine 9 methylation(H3K9me)-mediated Oct4 expression and can fully substitutevirally-delivered Oct4 for derivation of iPS cells in some cells Shi etal., Cell Stem Cell. 2: 525-528, 2008).

Alternatively, a short-hairpin RNA (shRNA) is used to knockdown ofexpression G9a. Such shRNA has been shown to result in demethylation ofOct4 promoter and partial reactivation of Oct4 expression (Ma et al.,Stem Cells. 26: 2131-2141, 2008).

In another example, an L-channel calcium agonist (e.g., Bayk8644 fromTocris Bioscience) is used in combination with a G9a antagonist (e.g.,BIX) to substitute for or complement Sox2 and cMyc (Shi et al., CellStem Cell. 3: 568-574, 2008).

In another example, a potency determining factor is a MEK inhibitor.Chemical inhibition of MEK (e.g., using PD0325901 from Cayman Chemical),which is responsible for somatic cell cycle progression, seven to ninedays after Oct4/Klf4 infection, and continually for several days (e.g.,5 days), results in enhanced growth of reprogrammed iPS colonies withhigher Oct4 expression (Shi et al., 2008 supra).

In a further example, a potency determining factor is Wnt3a.Extracellular Wnt3a can stimulate β-catenin-mediated induction ofendogenous cMyc expression in target cells, producing a dramaticimprovement in reprogramming efficiency (Marson et al., 2008).

In another example, a potency determining factor is okadaic acid.Okadaic acid (OA) is a potent inhibitor of protein serine/threoninephosphatase 2A (PP2A). PP2A dephosphorylates specific serine residues incMyc and targets it for rapid ubiquitin-regulated degradation. alsoelicits increased Klf4, which in turn binds OA-responsive elements inthe cMyc promoter eliciting upregulation of cMyc gene expression. OA'sadditional inhibitory effect on translation, through repression of EIFα,may lead to an initial accumulation of mRNA transcript and subsequentdelivery of bolus amounts of translated protein upon OA withdrawal.

In another example, a potency determining factor is Kenpaullone.Replacement of Klf4 with Kenpaullone, a broad spectrum protein kinaseinhibitor, to Oct4/Sox2/cMyc retrovirus expressing MEF generates Oct4selectable iPS cells able to contribute to germline-competent chimeras(Lyssiotis et al., Proc. Natl. Acad. Sci. USA 106: 8912-8917, 2009).

In a further example, a potency determining factor is a histinedeacetylase inhibitor. One hundred-fold improvements in iPSreprogramming efficiency of murine fibroblasts to iPS cells have beenobserved through chemical inhibition of histone deacetylase activity(Huangfu et al., Nat Biotech. 26: 795-797, 2008; Huangfu et al., NatBiotech. 26: 1269-1275, 2008). For example, valproic acid improvesreprogramming efficiency of genetic reprogramming.

In a further example, a potency determining factor is a DNA methylaseinhibitor.

b) Protein Delivery

Like use of small molecule compounds, protein delivery is an attractiveapproach to iPS cell generation due to its reversibility.

In one example, a protein potency determining factor is conjugated to aprotein transduction domain so as to facilitate intracellular(preferably intranuclear) entry. Protein transduction domains are knownin the art and include, for example, polyarginine, HIV Tat basic domain,antannapedia (e.g., as described in Jones et al., Br J Pharmacol.,145:1093-102, 2005. For example, E. coli expressed recombinant proteinsincorporating a poly-arginine targeting sequence linked to potencydetermining factors capable of converting MEF to iPS cells.

Methods for producing proteins are known in the art and/or described inSambrook et al., Molecular Cloning: A Laboratory Manual, Cold SpringHarbour Laboratory Press (1989) or Ausubel et al., (editors), CurrentProtocols in Molecular Biology, Greene Pub. Associates andWiley-Interscience (1988, including all updates until present).

c) Gene Silencing Strategies

In one example, a potency determining factor is a nucleic acid-basedcompound that silences or reduces expression of an endogenous gene.

In one example, a potency determining factor is a microRNA (miRNA).miRNAs are single-stranded, non-coding RNAs that regulate numerousbiological processes primarily through bonding target transcript in asequence-specific manner. miRNA are initially expressed as a primarytranscript, subsequently cleaved to release the active miRNA thatcomplexes with the RNA-induced silencing complex (RISC) to initiaterepression of translation. Transfection of miR-294 on days 0 and 6post-retroviral infection can replace cMyc to 75% efficiency (Judson etal., Nat. Biotech. 27: 459-461, 2009).

siRNA knockdown of Dnmtl can aid cells transgress from partially tofully reprogrammed and increase reprogramming efficiency 4-fold(Mikkelsen et al., Nature. 454: 49-55, 2008). Similarly, short-hairpinRNA (shRNA) knockdown of G9a, a histone methyltransferase involved inOct4 deactivation in post-implantation embryos in vivo, results indemethylation of the Oct4 promoter and partial reactivation (see above).Addition of p53 siRNA to adult foreskin fibroblasts, in concert withOct4/Sox2/Klf4 infection, increases efficiency, alone or in combinationwith additional treatments (Zhao et al., Cell Stem Cell. 3:475-479,2008).

The skilled artisan will be aware of suitable RNA-based compounds.Exemplary compounds include an antisense polynucleotide, a ribozyme, aPNA, an interfering RNA, a siRNA, short hairpin RNA a microRNA.

Antisense Polynucleotides

The term “antisense polynucleotide” shall be taken to mean a DNA or RNA,or combination thereof that is complementary to at least a portion of aspecific mRNA molecule encoding a polypeptide as described herein in anyembodiment and capable of interfering with a post-transcriptional eventsuch as mRNA translation. The use of antisense methods is known in theart (see for example, Hartmann and Endres, Manual of AntisenseMethodology, Kluwer (1999)).

An antisense polynucleotide of the invention will hybridize to a targetpolynucleotide under physiological conditions. Antisense polynucleotidesinclude sequences that correspond to the structural genes or forsequences that effect control over gene expression or splicing. Forexample, the antisense polynucleotide may correspond to the targetedcoding region of the genes of the invention, or the 5′-untranslatedregion (UTR) or the 3′-UTR or combination of these. It may becomplementary in part to intron sequences, which may be spliced outduring or after transcription, preferably only to exon sequences of thetarget gene. The length of the antisense sequence should be at least 19contiguous nucleotides, preferably at least 50 nucleotides, and morepreferably at least 100, 200, 500 or 1000 nucleotides of a targetnucleic acid or a structural gene encoding same. The full-lengthsequence complementary to the entire gene transcript may be used. Thelength is most preferably 100-2000 nucleotides. The degree of identityof the antisense sequence to the targeted transcript should be at least90% and more preferably 95-100%.

Catalytic Polynucleotides

The term “catalytic polynucleotide/nucleic acid” refers to a DNAmolecule or DNA-containing molecule (also known in the art as a“deoxyribozyme” or “DNAzyme”) or an RNA or RNA-containing molecule (alsoknown as a “ribozyme” or “RNAzyme”) which specifically recognizes adistinct substrate and catalyses the chemical modification of thissubstrate. The nucleic acid bases in the catalytic nucleic acid can bebases A, C, G, T (and U for RNA).

Typically, the catalytic nucleic acid contains an antisense sequence forspecific recognition of a target nucleic acid, and a nucleic acidcleaving enzymatic activity (also referred to herein as the “catalyticdomain”). The types of ribozymes that are particularly useful in thisinvention are a hammerhead ribozyme and a hairpin ribozyme.

RNA Interference

RNA interference (RNAi) is useful for specifically inhibiting theproduction of a particular protein. Although not wishing to be limitedby theory, Waterhouse et al., (1998) have provided a model for themechanism by which dsRNA (duplex RNA) can be used to reduce proteinproduction. This technology relies on the presence of dsRNA moleculesthat contain a sequence that is essentially identical to the mRNA of thegene of interest or part thereof. Conveniently, the dsRNA can beproduced from a single promoter in a recombinant vector or host cell,where the sense and anti-sense sequences are flanked by an unrelatedsequence which enables the sense and anti-sense sequences to hybridizeto form the dsRNA molecule with the unrelated sequence forming a loopstructure. The design and production of suitable dsRNA molecules for thepresent invention is well within the capacity of a person skilled in theart, particularly considering WO99/32619, WO99/53050, WO99/49029, andWO01/34815.

The length of the sense and antisense sequences that hybridize shouldeach be at least 19 contiguous nucleotides, preferably at least 30 or 50nucleotides, and more preferably at least 100, 200, 500 or 1000nucleotides. The full-length sequence corresponding to the entire genetranscript may be used. The lengths are most preferably 100-2000nucleotides. The degree of identity of the sense and antisense sequencesto the targeted transcript should be at least 85%, preferably at least90% and more preferably 95-100%.

Preferred small interfering RNA (“siRNA”) molecules comprise anucleotide sequence that is identical to about 19-23 contiguousnucleotides of the target mRNA. Preferably, the siRNA sequence commenceswith the dinucleotide AA, comprises a GC-content of about 30-70%(preferably, 30-60%, more preferably 40-60% and more preferably about45%-55%), and does not have a high percentage identity to any nucleotidesequence other than the target in the genome of the mammal in which itis to be introduced, for example as determined by standard BLAST search.

Culture Conditions

Pluripotent cells and/or reprogrammed cells and/or cells undergoingreprogramming can be cultured in any medium used to support growth ofpluripotent cells. Typical culture medium includes, but is not limitedto, a defined medium, such as TeSR™ (StemCell Technologies, Inc.;Vancouver, Canada), mTeSR™ (StemCell Technologies, Inc.) and StemLine®serum-free medium (Sigma; St. Louis, Mo.), as well as conditionedmedium, such as mouse embryonic fibroblast (MEF)-conditioned medium.Additional media include a base medium, e.g., DMEM or DMEM-F12supplemented with KoSR (Invitrogen Corporation). Alternatively, Silva etal., PLOS Biology, 6: e253, 2008 describes a medium useful for producingreprogrammed cells and maintaining reprogrammed cells in anundifferentiated state, e.g., comprising an inhibitor of MAPK signallingand glycogen synthase kinase-3 signaling and leukemia inhibitory factor(LIF). As used herein, a “defined medium” refers to a biochemicallydefined formulation comprised solely of biochemically-definedconstituents. A defined medium may also include solely constituentshaving known chemical compositions. A defined medium may further includeconstituents derived from known sources. As used herein, “conditionedmedium” refers to a growth medium that is further supplemented withsoluble factors from cells cultured in the medium. Alternatively, cellscan be maintained on MEFs in culture medium.

Cell cultures are preferably incubated at about 37° C. in a humidifiedincubator. Cell culture conditions can vary considerably for the cellsof the present invention, however, in some embodiments, the cells aremaintained in an environment suitable for cell growth, e.g., comprising5% O₂, 10% CO₂, 85% N₂ or comprising 10% CO₂ in air.

In another embodiment, cells are cultured on or within a matrix, e.g.,an extracellular matrix, e.g., Matrigel™, laminin, collagen, Culturex®,etc. In other embodiments, the cells may be cultured in the presence ofan extracellular matrix. Suitable procedures for proliferating cells inthe presence of such matrices are described, for example, in U.S. Pat.No. 7,297,539.

Isolation or Enrichment of Cells

The following methods are useful for isolation or enrichment of Stro-1⁺cells and/or reprogrammed/pluripotent cells, e.g., by detecting markersdescribed herein or known in the art.

One exemplary approach to enrich for the desired cells is magnetic beadcell sorting (MACS) or any other cell sorting method making use ofmagnetism, e.g., Dynabeads®. The conventional MACS procedure isdescribed by Miltenyi et al. (Cytometry 11: 231-238, 1990). In thisprocedure, cells are labelled with magnetic beads bound to an antibodyor other compound that binds to a cell surface marker or protein and thecells are passed through a paramagnetic separation column or exposed toanother form of magnetic field. The separation column is placed in astrong magnet, thereby creating a magnetic field within the column.Cells that are magnetically labeled are trapped in the column; cellsthat are not pass through. The trapped cells are then eluted from thecolumn.

Cells of the invention can be enriched, for example, from a suitablebodily reservoir, such as described above, using MACS to separate cellsexpressing a suitable protein. The sample is incubated withimmunomagnetic beads that bind to the protein. Following incubation,samples are washed and resuspended and passed through a magnetic fieldto remove cells bound to the immunomagnetic beads, and cells bound tothe beads collected. These techniques are equally applicable to negativeselection, e.g., removal of cells expressing an undesirable marker,i.e., undesirable cells. Such a method involves contacting a populationof cells with a magnetic particle labelled with a compound that binds toa cell surface marker expressed at detectable levels on the undesirablecell type(s). Following incubation, samples are washed and resuspendedand passed through a magnetic field to remove cells bound to theimmunomagnetic beads. The remaining cells depleted of the undesirablecell type(s) are then collected.

In another embodiment, a compound that binds to a protein or cellsurface marker is immobilized on a solid surface and a population ofcells is contacted thereto. Following washing to remove unbound cells,cells bound to the compound can be recovered, e.g., eluted, therebyisolating or enriching for cells expressing the protein to which thecompound binds. Alternatively, cells that do not bind to the compoundcan be recovered if desired.

In a preferred embodiment, cells are isolated or enriched usingfluorescence activated cell sorting (FACS). FACS is a known method forseparating particles, including cells, based on the fluorescentproperties of the particles and described, for example, in Kamarch,Methods Enzymol, 151:150-165, 1987). Generally, this method involvescontacting a population of cells with compounds capable of binding toone or more proteins or cell surface markers, wherein compounds thatbind to distinct markers are labelled with different fluorescentmoieties, e.g., fluorophores. The cells are entrained in the center of anarrow, rapidly flowing stream of liquid. The flow is arranged so thatthere is a separation between cells relative to their diameter. Avibrating mechanism causes the stream of cells to break into individualdroplets. The system is adjusted so that there is a low probability ofmore than one cell being in a droplet. Just before the stream breaksinto droplets the flow passes through a fluorescence measuring stationwhere the fluorescent character of interest of each cell is measured,e.g., whether or not a labelled compound is bound thereto. An electricalcharging ring is placed at the point where the stream breaks intodroplets. A charge is placed on the ring based on the immediately priorfluorescence intensity measurement and the opposite charge is trapped onthe droplet as it breaks from the stream. The charged droplets then fallthrough an electrostatic deflection system that diverts droplets intocontainers based upon their charge, e.g., into one container if alabelled compound is bound to the cell and another container if not. Insome systems the charge is applied directly to the stream and thedroplet breaking off retains charge of the same sign as the stream. Thestream is then returned to neutral after the droplet separates.

Differentiation of Cells

Reprogrammed cells or pluripotent cells of the invention can be used toprepare populations of differentiated cells of various commercially andtherapeutically important tissue types. In general, this is accomplishedby expanding the cells to the desired number. Thereafter, they arecaused to differentiate according to any of a variety of differentiationstrategies. For example, highly enriched populations of cells of theneural lineage can be generated by changing the cells to a culturemedium containing one or more neurotrophins (such as neurotrophin 3 orbrain-derived neurotrophic factor), one or more mitogens (such asepidermal growth factor, bFGF, PDGF, IGF 1, and erythropoietin), or oneor more vitamins (such as retinoic acid, ascorbic acid). Alternatively,multipotent neural stem cells can be generated through the embryoid bodystage and maintained in a chemically defined medium containing bFGF.Cultured cells are optionally separated based on whether they express anerve precursor cell marker such as nestin, Musashi, vimentin, A2B5,nurr1, or NCAM. Using such methods, neural progenitor/stem cells can beobtained having the capacity to generate both neuronal cells (includingmature neurons) and glial cells (including astrocytes andoligodendrocytes). Alternatively, replicative neuronal precursors can beobtained that have the capacity to form differentiated cell populations.

Cells highly enriched for markers of the hepatocyte lineage can bedifferentiated from reprogrammed or pluripotent cells by culturing thestem cells in the presence of a histone deacetylase inhibitor such asn-butyrate. The cultured cells are optionally cultured simultaneously orsequentially with a hepatocyte maturation factor such as EGF, insulin,or FGF.

Reprogrammed or pluripotent cells can also be used to generate cellsthat have characteristic markers of cardiomyocytes and spontaneousperiodic contractile activity. Differentiation in this way isfacilitated by nucleotide analogs that affect DNA methylation (such as5-aza-deoxy-cytidine), growth factors, and bone morphogenic proteins.The cells can be further enriched by density-based cell separation, andmaintained in media containing creatine, carnitine, and taurine.

Reprogrammed or pluripotent cells can be directed to differentiate intomesenchymal cells or chondrogenic cells in a medium containing a bonemorphogenic protein (BMP), a ligand for the human TGF-beta receptor, ora ligand for the human vitamin D receptor. The medium may furthercomprise dexamethasone, ascorbic acid-2-phosphate, and sources ofcalcium and phosphate. In preferred embodiments, derivative cells havephenotypic features of cells of the osteoblast lineage.

As will be appreciated, differentiated cells derived from reprogrammedor pluripotent cells can be also be used for tissue reconstitution orregeneration in a human patient in need thereof. The cells areadministered in a manner that permits them to graft to the intendedtissue site and reconstitute or regenerate the functionally deficientarea. For instance, neural precursor cells can be transplanted directlyinto parenchymal or intrathecal sites of the central nervous system,according to the disease being treated. The efficacy of neural celltransplants can be assessed in a rat model for acutely injured spinalcord, as described by McDonald, et al. ((1999) Nat. Med., vol. 5:1410)and Kim, et al. ((2002) Nature, vol. 418:50). Successful transplantswill show transplant-derived cells present in the lesion 2-5 weekslater, differentiated into astrocytes, oligodendrocytes, and/or neurons,and migrating along the spinal cord from the lesioned end, and animprovement in gait, coordination, and weight-bearing.

Similarly, the assignee of the instant application has demonstrated theutility of administering mesenchymal stem cells for the treatment ofbone fractures or cartilage injury.

Similarly, the efficacy of cardiomyocytes can be assessed in a suitableanimal model of cardiac injury or dysfunction, e.g., an animal model forcardiac cryoinjury where about 55% of the left ventricular wall tissuebecomes scar tissue without treatment (Li, et al. (1996), Ann. Thorac.Surg., vol. 62:654; Sakai, et al. (1999), Ann. Thorac. Surg., vol.8:2074; Sakai, et al. (1999), J. Thorac. Cardiovasc. Surg., vol.118:715). Successful treatment will reduce the area of the scar, limitscar expansion, and improve heart function as determined by systolic,diastolic, and developed pressure (Kehat, et al. (2004)). Cardiac injurycan also be modeled, for example, using an embolization coil in thedistal portion of the left anterior descending artery (Watanabe, et al.(1998), Cell Transplant., vol. 7:239), or by ligation of the leftanterior descending coronary artery (Min, et al. (2002), J. Appl.Physiol., vol. 92:288). Efficacy of treatment can be evaluated byhistology and cardiac function. Cardiomyocyte preparations embodied inthis invention can be used in therapy to regenerate cardiac muscle andtreat insufficient cardiac function.

Liver function can also be restored by administering hepatocytes andhepatocyte precursors differentiated from, for example, primatepluripotent stem cells grown in accordance with this invention. Thesedifferentiated cells can be assessed in animal models for ability torepair liver damage. One such example is damage caused byintraperitoneal injection of D-galactosamine (Dabeva, et al. (1993), Am.J. Pathol., vol. 143:1606). Treatment efficacy can be determined byimmunocytochemical staining for liver cell markers, microscopicdetermination of whether canalicular structures form in growing tissue,and the ability of the treatment to restore synthesis of liver-specificproteins. Liver cells can be used in therapy by direct administration,or as part of a bioassist device that provides temporary liver functionwhile the subject's liver tissue regenerates itself, for example,following fullminant hepatic failure.

Cellular Compositions

In one example of the present invention, reprogrammed or pluripotentcells and/or cells differentiated therefrom are administered in the formof a composition or formulated into such a composition. Preferably, sucha composition comprises a pharmaceutically acceptable carrier and/orexcipient.

The terms “carrier” and “excipient” refer to compositions of matter thatare conventionally used in the art to facilitate the storage,administration, and/or the biological activity of an active compound(see, e.g., Remington's Pharmaceutical Sciences, 16th Ed., MacPublishing Company (1980). A carrier may also reduce any undesirableside effects of the active compound. A suitable carrier is, for example,stable, e.g., incapable of reacting with other ingredients in thecarrier. In one example, the carrier does not produce significant localor systemic adverse effect in recipients at the dosages andconcentrations employed for treatment.

Suitable carriers for this invention include those conventionally used,e.g., water, saline, aqueous dextrose, lactose, Ringer's solution, abuffered solution, hyaluronan and glycols are preferred liquid carriers,particularly (when isotonic) for solutions. Suitable pharmaceuticalcarriers and excipients include starch, cellulose, sodium stearate,glycerol monostearate, sodium chloride, glycerol, propylene glycol,water, ethanol, and the like.

In another example, a carrier is a media composition, e.g., in which acell is grown or suspended. Preferably, such a media composition doesnot induce any adverse effects in a subject to whom it is administered.

Preferred carriers and excipients do not adversely affect the viabilityof a cell and/or the ability of a cell to exert a biological effect andpreferably a beneficial effect.

In one example, the carrier or excipient provides a buffering activityto maintain the cells and/or soluble factors at a suitable pH to therebyexert a biological activity, e.g., the carrier or excipient is phosphatebuffered saline (PBS). PBS represents an attractive carrier or excipientbecause it interacts with cells and factors minimally and permits rapidrelease of the cells and factors, in such a case, the composition of theinvention may be produced as a liquid for direct application to theblood stream or into a tissue or a region surrounding or adjacent to atissue, e.g., by injection.

reprogrammed or pluripotent cells and/or cells differentiated therefromcan also be incorporated or embedded within scaffolds that arerecipient-compatible and which degrade into products that are notharmful to the recipient. These scaffolds provide support and protectionfor cells that are to be transplanted into the recipient subjects.Natural and/or synthetic biodegradable scaffolds are examples of suchscaffolds.

A variety of different scaffolds may be used successfully in thepractice of the invention. Preferred scaffolds include, but are notlimited to biological, degradable scaffolds. Natural biodegradablescaffolds include collagen, fibronectin, and laminin scaffolds. Suitablesynthetic material for a cell transplantation scaffold should be able tosupport extensive cell growth and cell function. Such scaffolds may alsobe resorbable. Suitable scaffolds include polyglycolic acid scaffolds,e.g., as described by Vacanti, et al. J. Ped. Surg. 23:3-9 1988; Cima,et al. Biotechnol. Bioeng. 38:145 1991; Vacanti, et al. Plast. Reconstr.Surg. 88:753-9 1991; or synthetic polymers such as polyanhydrides,polyorthoesters, and polylactic acid.

In another example, the cells may be administered in a gel scaffold(such as Gelfoam from Upjohn Company.

The cellular compositions useful for the present invention may beadministered alone or as admixtures with other cells. Cells that may beadministered in conjunction with the compositions of the presentinvention include, but are not limited to, other multipotent orpluripotent cells or stem cells, or bone marrow cells. The cells ofshortly prior to administration, or they may be co-cultured together fora period of time prior to administration.

Preferably, the composition comprises an effective amount or atherapeutically or prophylactically effective amount of cells. Forexample, the composition comprises about 1×10⁵ reprogrammed orpluripotent cells and/or cells differentiated therefrom/kg to about1×10⁷ reprogrammed or pluripotent cells and/or cells differentiatedtherefrom/kg or about 1×10⁶ reprogrammed or pluripotent cells and/orcells differentiated therefrom/kg to about 5×10⁶ reprogrammed orpluripotent cells and/or cells differentiated therefrom/kg. The exactamount of cells to be administered is dependent upon a variety offactors, including the age, weight, and sex of the patient, and theextent and severity of disorder to be treated.

In some embodiments, cells are contained within a chamber that does notpermit the cells to exit into a subject's circulation, however thatpermits factors secreted by the cells to enter the circulation. In thismanner soluble factors may be administered to a subject by permittingthe cells to secrete the factors into the subject's circulation. Such achamber may equally be implanted at a site in a subject to increaselocal levels of the soluble factors.

In some embodiments of the invention, it may not be necessary ordesirable to immunosuppress a patient prior to initiation of therapywith cellular compositions. Accordingly, transplantation withallogeneic, or even xenogeneic, reprogrammed or pluripotent cells and/orcells differentiated therefrom may be tolerated in some instances.

However, in other instances it may be desirable or appropriate topharmacologically immunosuppress a patient prior to initiating celltherapy. This may be accomplished through the use of systemic or localimmunosuppressive agents, or it may be accomplished by delivering thecells in an encapsulated device. The cells may be encapsulated in acapsule that is permeable to nutrients and oxygen required by the celland therapeutic factors the cell is yet impermeable to immune humoralfactors and cells. Preferably the encapsulant is hypoallergenic, iseasily and stably situated in a target tissue, and provides addedprotection to the implanted structure. These and other means forreducing or eliminating an immune response to the transplanted cells areknown in the art. As an alternative, the cells may be geneticallymodified to reduce their immunogenicity.

Screening Methods

The present invention also provides a method for identifying orisolating a compound that induces or enhances reprogramming of a Stro-1⁺multipotential cell and/or progeny cell thereof said method comprisingcontacting a Stro-1⁺ multipotential cell and/or progeny cell thereofwith a compound for a time and under conditions sufficient forre-programming to occur if the compound induces or enhancesreprogramming and determining whether or not the cell is reprogrammed.

In one example, the method comprises:

(i) contacting a population enriched for Stro-1⁺ multipotential cellsand/or progeny cells thereof with a compound for a time and underconditions sufficient for re-programming to occur if the compoundinduces or enhances reprogramming and determining the number ofreprogrammed cells; and(ii) determining the number of reprogrammed cells in a populationenriched for Stro-1⁺ multipotential cells and/or progeny cells thereofthat have not been contacted with the compound,

wherein an increased number of reprogrammed cells at (i) compared to(ii) indicates that the compound induces or enhances reprogramming of aStro-1⁺ multipotential cell and/or progeny cell thereof.

In one example, the method is performed in the presence of one or morepotency determining factors, e.g., as described herein.

The present invention also provides a method for isolating oridentifying a compound that induces or enhances differentiation of areprogrammed or pluripotent cell into a desired cell type, said methodcomprising contacting a reprogrammed or pluripotent cell produced byperforming a method as described herein according to any embodiment anddetermining whether or not the cell differentiates into a desired celltype.

Preferably, the method comprises:

(i) contacting a population enriched for reprogrammed or pluripotentcell produced by performing a method as described herein according toany embodiment with a compound for a time and under conditionssufficient for cell differentiation to occur and determining the numberof cells of the desired cell type; and(ii) determining the number of cells of the desired cell type producedby culturing reprogrammed or pluripotent cell produced by performing amethod as described herein according to any embodiment under the sameconditions however in the absence of the compound,wherein an increased number of cells of the desired cell type at (i)compared to (ii) indicates that the compound induces or enhancesdifferentiation into the desired cell type.

The present invention also provides a method for identifying orisolating a compound useful for treating a condition, the methodcomprising:

(i) performing a method as described herein according to any embodimentto produce a pluripotent cell or population thereof from a subjectsuffering from the condition; and(ii) contacting the cell or population with a test compound anddetermining its effect on one or more symptoms of the condition, whereina compound that improves or alleviates a symptom of the condition isuseful for treating the condition.

In on example, the method comprises:

(a) differentiating the pluripotent cell or population thereof intocells affected in the condition; and(b) contacting the cells at (a) with the test compound and determiningits effect on one or more symptoms of the condition, wherein a compoundthat improves or alleviates a symptom of the condition is useful fortreating the condition.

Such a method is useful not only for identifying or isolating newcompounds for treating a condition, but also for identifying whether ornot a subject is likely to respond to treatment with an existingtherapeutic/prophylactic compound.

The skilled artisan will be aware of suitable methods fordifferentiating cells, e.g., based on the disclosure herein and/orsuitable conditions and/or symptoms of those conditions. For example, acondition is cystic fibrosis and the symptom is secretions from a lungcell; or a neurodegenerative condition (e.g., Alzheimer's disease orHuntington's disease) and the symptom is neurodegeneration orplaque/intracellular aggregate formation; or a cardiac condition and thesymptom is cardiomyocyte contractility.

The present invention also contemplates methods for identifyingcompounds having reduced toxicity to a cell or tissue type, e.g., todetermine therapeutic compounds having a reduced risk of toxicity. Forexample, the present invention provides a method comprising:

(i) performing a method as described herein according to any embodimentto produce a pluripotent cell or population thereof;(ii) differentiating the pluripotent cell or population thereof intocells of one or more specific lineages and/or into tissue;(iii) contacting the cells with a test compound; and(iv) determining the effect of the compound on cell viability and/orproliferation, wherein a compound that does not kill a cell or asignificant proportion of a population of cells or reduce proliferationis considered to have reduced toxicity.

Exemplary differentiated cells are blood cells, liver cells, kidneycells and heart cells.

Methods for determining the effect of a compound on cell viabilityand/or proliferation are known in the art and include a terminaldeoxynucleotidyl transferase-mediated biotinylated UTP nick end-labeling(TUNEL) assay, a trypan blue dye exclusion assay, a MTT assay, athymidine incorporation assay or a BrdU incorporation assay.

The skilled artisan will be aware from the foregoing that the presentinvention encompasses various methods for identifying and/or isolatingcompounds using a cell as described herein according to any embodiment.Suitable compounds for screening include, for example, antibodies,peptides or small molecules.

This invention also provides for the provision of information concerningthe identified or isolated compound. Accordingly, the screening methodsare further modified by:

(i) optionally, determining the structure of the compound; and(ii) providing the compound or the name or structure of the compoundsuch as, for example, in a paper form, machine-readable form, orcomputer-readable form.

Naturally, for compounds that are known albeit not previously tested fortheir function using a screen provided by the present invention,determination of the structure of the compound is implicit. This isbecause the skilled artisan will be aware of the name and/or structureof the compound at the time of performing the screen.

As used herein, the term “providing the compound” shall be taken toinclude any chemical or recombinant synthetic means for producing saidcompound or alternatively, the provision of a compound that has beenpreviously synthesized by any person or means. This clearly includesisolating the compound.

In a preferred embodiment, the compound or the name or structure of thecompound is provided with an indication as to its use e.g., asdetermined by a screen described herein.

The screening assays can be further modified by:

(i) optionally, determining the structure of the compound;(ii) optionally, providing the name or structure of the compound suchas, for example, in a paper form, machine-readable form, orcomputer-readable form; and(iii) providing the compound.

In a preferred embodiment, the synthesized compound or the name orstructure of the compound is provided with an indication as to its usee.g., as determined by a screen described herein.

In one embodiment, the compound is provided in a library of compounds,each of which or a subset of which may be separated from other members(i.e., physically isolated). In such cases, a compound is isolated fromthe library by its identification, which then permits a skilled personto produce that compound in isolation, e.g., in the absence of othermembers of the library.

The present invention is described further in the following non-limitingexamples.

Example 1 Production of Reprogrammed Cells from Stro-1+ MultipotentialProgenitor Cells 1.1 Stro-1⁺ Multipotential Progenitor Cell EnrichedPopulations

Stro-1+ multipotential progenitor cells are obtained from varioustissues, including bone marrow, adipose tissue and dental pulp tissue.For comparison of reprogramming efficiencies of Stro-1⁺ multipotentialprogenitor cells derived from different sites, cells from each of thesetissues are enriched for Stro-1^(Bright) cells by immunoselection usingthe STRO3 mAb, then culture-expanded and cryopreserved in ProFreeze™-CDM(Lonza, USA), essentially as described in Gronthos and ZannettinoMethods Mol Biol. 449:45-57, 2008). For comparison of reprogrammingefficiencies of Stro-1⁺ multipotential progenitor cells derived from thesame site using different immunoselection methods, paired bone marrowsamples from the same donor are enriched for Stro-1^(Bright) cells byimmunoselection using either STRO3 or STRO1 mAbs, culture-expanded andcryopreserved in ProFreeze™-CDM (Lonza, USA), For all studies, Passage 4cells are thawed and constituted in vehicle for immediate use.

1.2 Lentiviral Vector Packaging and Production

Transgene-expressing lentivirus vector is produced in 293FT cell lines(Invitrogen). 293T is a fast-growing, highly transferable clonal variantderived from transformed 293 embryonal kidney cells, which contains thelarge T antigen for high-level expression of the packaging proteins thatcontribute to higher viral titers. For routine maintenance andexpansion, these cells are cultured in 293FT medium (DMEM/10% FBS, 2 mML-glutamine and 0.1 mM MEM Non-Essential Amino Acids) in the presence of500 μg/ml geneticin. For packaging, 293FT cells are collected bytrypsinization. Following removal of trypsin by centrifugation, thesecells are aliquoted into T75 flasks (15×106 cells/flask, and 6 flasksper construct) in 293FT medium without geneticin.

Co-transfection of lentiviral vector and two helper plasmids is carriedout with Superfect® transfection reagent (Qiagen) immediately followingcell aliquoting. The next day, the culture medium containing thetransfection mixture is replaced with fresh 293FT medium supplementedwith 1 mM sodium pyruvate (8 ml/flask). Lentivirus-containingsupernatant is collected around 48 to 72 hours after transduction. The293FT cell debris is removed from the supernatant by centrifugation for15 minutes at 4° C. To concentrate the lentivirus, the supernatant isfiltered through 0.4 μM cellulose acetate (CA) membrane (Cornington, 115ml low-protein binding), and ultracentrifuged in 70 ml sterilizedbottles (Beckman, Cat#355622, polycarbonate for 45Ti rotor only) for 2.5hours at 40° C. Following supernatant removal, PBS (˜300 μl for eachconstruct) is added to resuspend the pellet by rocking the centrifugetubes at 40 C for 8 to 14 hours, or at room temperature for 2 hours. Theremaining cell debris is removed by centrifugation, and the resuspendedlentivirus was aliquoted and stored at −80° C. Lentivirus carrysequences encoding one or more potency determining factors.

1.3 Reprogramming of Cells after Lentiviral transduction and Expressionof Potency-Determining Factors

Lentivirus encoding one or more potency-determining factor(s) (e.g.,Oct4; or a combination of Oct4 and Sox2; or a combination of Oct4, Sox2and at least one of Nanog and Lin28; or a combination of Oct4, Klf4 andc-Myc; or a combination of Oct4, Sox2 and Klf4; or a combination ofOCT4, Sox2, Klf4 and c-Myc; or a combination of Oct4, Sox2, Nanog andLin28; or a combination of Oct4, Sox2, Klf4, c-Myc, Nanog and Lin28) isadded to the cell culture after addition of polybrene carrier at a finalconcentration of about 6 μg/ml (Sigma).

The lentivirus-containing medium is replaced with fresh medium the nextday, and cells are cultured further in appropriate medium. Drugselection, if needed, is commenced the third day after transduction.

Cells are analyzed using cell-sorting methods before and after exposingthe somatic cells to the factors. Adherent cells are dissociated bytrypsin treatment (0.05% Trypsin/0.5 mM EDTA, Invitrogen), and fixed in2% paraformaldehyde for 20 minutes at room temperature. The cells arefiltered through a 40-μm mesh, and resuspended in FACS buffer (PBScontaining 2% FBS and 0.1% sodium azide). Cells grown in suspension werestained in the FACS buffer supplemented with 1 mM EDTA and 1% normalmouse serum (Sigma). Intracellular myeloperoxidase (MPO) staining isperformed using Fix & Perm® reagents (Caltag Laboratories; Burlingame,Calif.). About 100 μl of cell suspension containing 5×105 cells is usedin each labeling. Both primary and secondary antibody incubation (whereapplied) are carried out at room temperature for about 30 minutes.Control samples are stained with isotype-matched control antibodies.After washing, the cells are resuspended in about 300-500 μl of FACSbuffer, and analyzed on a FACSCalibur flow cytometer (BDIS; San Jose,Calif.) using CellQuest™ acquisition and analysis software (BDIS). Atotal of 20,000 events are acquired. Markers detected are selected fromSSEA-3, SSEA-3, SSEA-4, Tra-1-60, Tra-1-81, CD29, Tra-1-85, CD56, CD73,CD105, CD31 or CD34.

In some transductions and subsequent cultures cells are maintained inthe presence or valproic acid.

EB and teratoma formation are also used to demonstrate that thereprogrammed cells have a developmental potential to give rise todifferentiated derivatives of all three primary germ layers.

Example 2 Production of Reprogrammed Cells from Stro-1+ MultipotentialProgenitor Cells 2.1 Materials and Methods Stro-1+ Multipotent CellEnriched Populations

Cell populations enriched fro Stro-1⁺ multipotential progenitor cellswere obtained from bone marrow, adipose tissue and dental pulp tissue.For comparison of reprogramming efficiencies of Stro-1+ multipotentialprogenitor cells derived from different sites, cells from each of thesetissues were enriched for Stro-1^(Bright) cells by immunoselection usingthe STRO3 mAb, then culture-expanded and cryopreserved in ProFreeze™-CDM(Lonza, USA), essentially as described in Gronthos and ZannettinoMethods Mol Biol. 449:45-57, 2008). For comparison of reprogrammingefficiencies of Stro-1⁺ multipotential progenitor cells derived from thesame site using different immunoselection methods, paired bone marrowsamples from the same donor were enriched for Stro-1^(Bright) cells byimmunoselection using either STRO3 or STRO1 mAbs, culture-expanded andcryopreserved in ProFreeze™-CDM (Lonza, USA), For all studies, Passage 4cells were thawed and constituted in vehicle for immediate use.

Cell Lines

Platinum-A (Plat-A) cells, the viral packaging cells, were obtained fromCell Biolabs, Inc. Detroit 551 fibroblasts were positive controls forthe experiment.

Retroviral Production and iPS Cell Generation

Moloney-based retroviral vectors (pMXs) containing the human cDNAs ofOCT4, SOX2, KLF4 and cMYC were obtained from Addgene. 9 μg of eachplasmid was transfected into viral packaging Plat-A cells using Fugene 6(Roche). Virus-containing supernatants were collected 48 and 72 hpost-transfection and filtered through a 0.45 μm pore-size filter andsupplemented with 4 μg/ml of polybrene (Sigma). Target cells were plated24 h prior to infection at a density of 1×10³ to 5×10³cells/cm².Retroviral supernatants of four transcription factors were mixed inequal quantities and double infections were added to target cells at 24h and 48 h. The culture medium for the infected cells was changed to hEScell medium at day 4 post-infection. The cells were maintained in theculture with medium refreshment every day for up to 3 weeks or untilcells reached confluence.

Propagation of iPS Cells

To establish iPS cell lines, iPS cell colonies were picked-up based onhES cell-like colony morphology at about 3 weeks post-infection. Thepicked colonies were expanded on fresh mitotically inactivated MEFs inhES cell medium.

Maintenance of iPS Cells

Human iPS cells were cultured in DMEM supplemented with 20% FBS(Hyclone), 1 mM L-Glutamax, 0.1 mM non-essential amino acids, 0.1 mMβ-mercaptoethanol, 1% ITS, and 10 ng/ml bFGF (all from Invitrogen).Human iPS cells were refreshed daily with culture medium. Mechanicaldissociation was performed by dissecting iPS cells colonies into smallercell clumps using a 1 ml insulin syringe with 29G needle. The colonieswere transferred onto fresh mitotically-inactivated MEFs after 8 to 10days after infection. The iPS colonies were passaged every 7 to 10 daysthereafter by mechanical dissociation.

FACS Analysis

To estimate transfection efficiency of cells, pMXs-GFP retroviralvectors were also transfected to Plat-A cells using the same method asdescribed above. pMXs retroviruses containing the GFP cDNA were addedcells. The number of cells expressing GFP was evaluated by flowcytometry 48 h after infection. Cells were dissociated with 0.25%trypsin-EDTA (Invitrogen) for 5 min and were analysed using a flowcytometer (MoFLO).

Reprogramming Efficiency Assay

Adipose cells, dental pulp cells and MPCs were infected with 4 factorsas described in “Retroviral Production and iPS Cell Generation” above.Cells were maintained for 17 days with daily media changes. Cells werethen dissociated with trypsin, and fixed with 4% paraformaldehyde. Cellswere blocked with 2.5% (w/v) skim milk powder, 2% (v/v) goat serum inPBS. Cells were labelled with primary antibody (mouse anti-Oct4,anti-Nanog or anti-SSEA4) overnight at 4° C., then labeled with a goatanti mouse Alexa 488 secondary antibody for lhr at room temperature.Samples were analysed by FACS as described above to determine the numberof positively stained cells.

2.2 Results

All Stro-1⁺ multipotential progenitor enriched populations, irrespectiveof whether they were sourced from dental pulp, adipose tissues, or bonemarrow, and irrespective of whether they were immunoselected with STRO-3or STRO-1 mAbs, were able to be reprogrammed and to generate iPS celllines.

A summary of outcomes for reprogramming of various cells is shown inTable 1.

TABLE 1 Outcomes of cell reprogramming experiments Cell LineRoprogramming Outcomes % of total transfected cell population expressingAverage exogenous and GFP Total iPS colony reprogrammed infection countper plate genes Cell type efficiency Plate 1 Plate 2 Average Oct4 NanogDental Pulp 98.27 56 56 56 56.98 5 Adipose 71.17 20 24 22 55.79 9.57Bone marrow 91.85 0 1 0.5 35.89 21.6 Detroit 551 95.89 9 5 7 69.38 28.24

Transfection efficiencies of all cell types, as determined by a GFPreporter construct, was similar, ranging from 71.2-98.3%. Results fromstudies measuring the number of iPS colonies growing per plate indicatedsignificantly higher putative iPS cell colony formation for linesderived from cell populations enriched for Stro-1⁺ multipotentialprogenitor cells sourced from dental pulp and adipose tissues comparedwith lines derived from D551 fetal fibroblasts. In addition, iPS cellcolony formation for lines derived from cell populations enriched forStro-1⁺ multipotential progenitor cells sourced from dental pulp andadipose tissues was significantly higher than for lines derived fromStro-1+ multipotential progenitor cells from bone marrow. Average colonynumbers (per 50,000 cells plated) for dental pulp and adipose tissue (56and 22 respectively) were significantly higher than observed for D551fibroblasts (7) or bone marrow (0.5) (p<0.05, Chi Square test).

To examine whether the increased efficiency of iPS generation fromStro-1⁺ multipotential progenitor cells relative to D551 fibroblasts wasrelated to sustained expression of exogenously transfected genes orinduced endogenous genes, we next measured expression of Oct4 and Nanogin the total cultured transfected cell population. As shown in Table 1,transfected D551 fibroblasts demonstrated the highest levels ofsustained Oct4 expression (69%), transfected Stro-1+ multipotentialprogenitor cells sourced from dental pulp or adipose tissues hadintermediate levels of Oct4 expression (57% and 56%, respectively), andtransfected bone marrow Stro-1⁺ multipotential progenitor cells had thelowest level of Oct4 expression (36%).

Transfected populations of Stro-1+ multipotential progenitor cellssourced from dental pulp or adipose tissues had lower total numbers ofcells expressing Nanog (5% and 10%, respectively) than transfected D551fibroblasts (28%). For bone marrow Stro-1⁺ multipotential progenitorcells, similar patterns of Oct4 and Nanog expression were consistentlyseen irrespective of whether they were immunoselected from the samepaired bone marrow sample with a STRO-3 or a STRO-1 mAb (30% and 37%,respectively, for Oct4, and 17% and 21%, respectively, for Nanog).

In conjunction with previously published data (Chan et al., NatureBiotech. 27(11):1033-1037 (2009)) showing that induced Nanog expressioncan be associated with iPS-like colonies which are at an intermediatestage, but which do not necessarily progress to a definitive iPS stage,our findings that transfected Stro-1+ multipotential progenitor cellssourced from dental pulp or adipose tissues have lower Nanog expressionbut significantly higher iPS colony numbers than D551 fibroblastsindicate that Stro-1+ multipotential progenitor cells represent a morepermissive cell type for progression to definitive iPS colony formationfollowing exposure to potency factors.

Together, these results indicate that:

1) Despite similar Oct 4 expression after transfection, cell populationsenriched for Stro-1⁺ multipotential progenitor cells sourced from dentalpulp and adipose tissues produced iPS cell colonies more efficiently andwith greater numbers than control fibroblasts;2) Despite lower induced Nanog expression after transfection, cellpopulations enriched for Stro-1⁺ multipotential progenitor cells sourcedfrom dental pulp and adipose tissues produced definitive iPS cellcolonies more efficiently and with greater numbers than controlfibroblasts; and3) Tissue source can affect efficiency of iPS cell colony formation,since cell populations enriched for Stro-1⁺ multipotential progenitorcells sourced from dental pulp and adipose tissues produced iPS cellcolonies more efficiently than cell populations enriched for Stro-1+multipotential progenitor cells from bone marrow.

Immunofluorescence

iPS cell colonies from dental pulp were shown to express Oct4, Nanog,SSEA4, TRA1-60 and TRA1-81 by immunofluorescence. These cells were alsoshown to express alkaline phosphatase.

iPS cell colonies from adipose tissue were shown to express Oct4 byimmunofluorescence and to express alkaline phosphatase.

Gene Expression of iPS Cell Lines

Results of gene expression studies are represented in Table 2.

By way of summary, all Stro-1⁺ multipotential progenitor cell enrichedcell populations, irrespective of whether they were obtained from dentalpulp, adipose tissue, or bone marrow, endogenously expressed KLF4 andc-myc before infection. Without wishing to be bound by theory or mode ofaction endogenous expression of these potency factors by Stro-1⁺multipotential progenitor cells may in part explain the greaterefficiency of iPS generation using Stro-1⁺ multipotential progenitorcells than fibroblasts. However, additional factors may explain thegreater observed efficiency of Stro-1⁺ multipotential progenitor cellssourced from dental pulp or adipose tissues to generate iPS lines thanthose from bone marrow.

The established dental iPS cell lines expressed all endogenous genes Oct4, Sox 2, c-myc and Klf4. The exogenous Oct4 and c-myc were silenced atpassage 3 and 8 but Sox 2 and Klf4 remained expressed.

Adipose IPSCs at passage 2 only expressed endogenous Klf4. Exogenous Oct4 and c-myc remained unsilenced.

Bone marrow-MPCs at passage 2 did not show any endogenous geneexpressions. The only exogenous gene silenced in these cells was Sox2.

TABLE 2 RT-PCR characterisation of iPS cell lines. RT-PCR EndogenousGenes Exogenous Genes Cell Type Time Point B-actin Oct4 Sox2 KLF4 c-mycNanog Oct4 Sox2 KLF4 c-myc Dental No infection ++ − − + + − − − − −Infection 2 weeks ++ − + + + + ++ ++ + ++ Dental i1-2 ++ ++ ++ ++ ++ − −++ + − Adipose No infection ++ − − + + + − − − − Infection 2 weeks + −− + + + + ++ + + Adipose i1-1 + − − − − − + − + − i1-2 − − − − + + ++ +++ ++ i1-3 − − − + − − ++ − − ++ Bone No infection ++ − − + + − − − − −marrow Infection 2 weeks ++ − − − + − + ++ + + MPC i2-2 ++ − − − − − ++− + ++

1. A method of producing a reprogrammed cell, said method comprisingexposing Stro-1⁺ multipotential cells and/or progeny cells thereof toone or more potency-determining factors under conditions sufficient toreprogram the cells.
 2. A method of producing a reprogrammed cell, saidmethod comprising exposing a population of cells enriched for Stro-1⁺multipotential cells and/or progeny cells thereof to one or morepotency-determining factors under conditions sufficient to reprogram thecells.
 3. The method according to claim 1 or 2, wherein the Stro-1⁺multipotential cells and/or progeny cells thereof, or cell populationsenriched for Stro-1⁺ multipotential cells and/or progeny cells thereof,are derived from adipose tissue, dental pulp tissue, or bone marrow. 4.The method according to claim 1 or 2 additionally comprising culturingthe exposed cells to produce reprogrammed cells.
 5. The method accordingto claim 1 or 2 additionally comprising isolating the reprogrammedcells.
 6. The method according to any one of claims 1 to 5 comprisingculturing the exposed cells to obtain reprogrammed cells having broaderdifferentiation potential than the Stro-1⁺ multipotential cells and/orprogeny cells thereof.
 7. The method according to any one of claims 1 to6, wherein the one or more potency-determining factors are individuallyor collectively selected from the group consisting of Oct4, Sox2, Klf4,Nanog, Lin28, c-Myc, bFGF, SCF, TERT, SV40 large T antigen, HPV16E6,HPV16E7, Bmil, Fbx15, Eras, ECAT15-2, Tcl1, β-catenin, ECAT1, ESG1,Dnmt3L, ECAT8, Gdf3, Sox15, ECAT15-1, Fthl17, Sal14, Rex1, UTF1, Stella,Stat3 and Grb2 or a compound having the same or similar activity to oneor more of said factors.
 8. The method according to any one of claims 1to 7, wherein one or more potency determining factor(s) is a chemical, apeptide, a siRNA, a short hairpin RNA or a microRNA.
 9. The methodaccording to any one of claims 1 to 7, wherein the one or morepotency-determining factors are individually or collectively selectedfrom the group consisting of: (i) Oct4; (ii) a combination of Oct4 andSox2; (iii) a combination of Oct4, Sox2 and at least one of Nanog andLin28; (iv) a combination of Oct4, Klf4 and c-Myc; (v) a combination ofOct4, Sox2 and Klf4; (vi) a combination of OCT4, Sox2, Klf4 and c-Myc;(vii) a combination of Oct4, Sox2, Nanog and Lin28; (viii) a combinationof Oct4, Sox2, Klf4, c-Myc, Nanog and Lin28; and (ix) any one of (i) to(x) additionally in combination with a chemical, a peptide, a siRNA, ashRNA or a microRNA.
 10. The method according to any one of claims 1 to9, wherein the Stro-1⁺ multipotential cells and/or progeny cells thereofare obtained from a post-natal mammal.
 11. The method according to claim10, wherein the mammal is human.
 12. The method according to claim 1 or2, wherein exposing the Stro-1⁺ multipotential cells and/or progenycells thereof to one or more potency-determining factors comprisesintroducing nucleic acid comprising a sequence encoding one or morepotency-determining factors operably linked to a promoter into theStro-1⁺ multipotential cells and/or progeny cells thereof.
 13. Themethod according to claim 12, comprising administering a plurality ofnucleic acids each comprising a sequence encoding a distinctpotency-determining factor operably linked to a promoter.
 14. The methodaccording to claim 12 or 13, wherein the nucleic acid(s) are within oneor more vector(s).
 15. The method according to claim 14, wherein thevector(s) is(are) a viral vector(s).
 16. The method according to claim12, wherein the nucleic acid(s) do(es) not integrate into the genome ofthe Stro-1⁺ multipotential cells and/or progeny cells thereof.
 17. Themethod according to claim 1 or 2, wherein the reprogrammed cells arepluripotent.
 18. The method according to claim 1 or 2, wherein thereprogrammed cells (i) express a cell marker selected from the groupconsisting of Oct-4, Nanog, SSEA3, SSEA4, Tra-1-60 and Tra-1-81; (ii)exhibit morphology characteristic of pluripotent cells; and/or (iii)form teratomas when introduced into an immunocompromised animal.
 19. Acell produced by performing the method according to any one of claims 1to
 18. 20. A cell population enriched for pluripotent cells produced byperforming the method according to the method of any one of claims 1 to18.
 21. The enriched population of cells according to claim 20, whereinthe pluripotent cells account for at least 60% of the population.
 22. Acell or population of cells differentiated from the cell or populationaccording to any one of claims 18 to
 21. 23. A Stro-1⁺ multipotentialcell and/or progeny cell thereof comprising a nucleic acid encoding apotency determining factor operably linked to a heterologous promoter.24. Use of the cell or population according to any one of claims 19 to23 in medicine.
 25. A method of treating or preventing a disease ordisorder, the method comprising administering the cell or populationaccording to any one of claims 19 to 23 to a subject in need thereof.26. A method of screening for compounds useful in the treatment orprevention of a disease or disorder, the method comprising exposing thecell or population according to any one of claims 19 to 23 to saidcompounds.